Starting phenix.real_space_refine
on Wed Mar 12 15:06:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yut_39582/03_2025/8yut_39582.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yut_39582/03_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_39582/03_2025/8yut_39582.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yut_39582/03_2025/8yut_39582.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yut_39582/03_2025/8yut_39582.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yut_39582/03_2025/8yut_39582.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.21, per 1000 atoms: 0.63
  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: 2.07
  Conformation dependent library (CDL) restraints added in 880.0 milliseconds
  

  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: 0.87
  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: 2.20

  Time building geometry restraints manager: 2.38 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.360
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.650
-------------------------------------------------------------------------------
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   8388  Z= 0.524
  Angle     :  0.811  18.419  11373  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (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
 TRP   0.020   0.002   TRP R 222 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.018   0.002   PHE N  68 
 TYR   0.026   0.002   TYR N 115 
 ARG   0.007   0.000   ARG N 118 

*********************** 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  : 0.836 
Fit side-chains
   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: 0.5778 (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: 1.2257
  time to fit residues: 211.2617
Evaluate side-chains
  103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4163 r_free = 0.4163 target = 0.191404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.150662 restraints weight = 8383.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 1.95
r_work: 0.3572 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8388  Z= 0.186
  Angle     :  0.538   9.666  11373  Z= 0.291
  Chirality :  0.042   0.145   1301
  Planarity :  0.004   0.071   1443
  Dihedral  :  4.947  51.419   1207
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  8.08 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.26), residues: 1025
  helix:  2.23 (0.25), residues: 410
  sheet:  1.10 (0.34), residues: 209
  loop : -0.20 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 222 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.014   0.002   PHE A 212 
 TYR   0.015   0.002   TYR B 105 
 ARG   0.015   0.001   ARG B 197 

*********************** 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
  135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6856 (mtmt) cc_final: 0.6302 (mmmt)
REVERT: A  232 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8132 (ptp90)
REVERT: B  186 ASP cc_start: 0.8152 (m-30) cc_final: 0.7852 (m-30)
REVERT: B  195 ASP cc_start: 0.6983 (p0) cc_final: 0.6732 (p0)
REVERT: B  197 ARG cc_start: 0.7324 (mmm160) cc_final: 0.7038 (mmp80)
REVERT: B  217 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6164 (mmp)
REVERT: B  259 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7387 (mt0)
REVERT: B  291 ASP cc_start: 0.6871 (m-30) cc_final: 0.6671 (p0)
REVERT: G   21 MET cc_start: 0.6368 (ttp) cc_final: 0.5464 (tmt)
REVERT: N    4 LEU cc_start: 0.7880 (mt) cc_final: 0.7574 (mt)
REVERT: N   21 SER cc_start: 0.8650 (t) cc_final: 0.8406 (t)
REVERT: N   25 SER cc_start: 0.7046 (OUTLIER) cc_final: 0.6757 (p)
REVERT: N  110 VAL cc_start: 0.8521 (t) cc_final: 0.8113 (m)
REVERT: R  122 ASP cc_start: 0.8275 (p0) cc_final: 0.7800 (p0)
  outliers start: 23
  outliers final: 9
  residues processed: 125
  average time/residue: 1.1391
  time to fit residues: 152.5433
Evaluate side-chains
  107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
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  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    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 56 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.189254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.148880 restraints weight = 8508.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 1.99
r_work: 0.3556 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8388  Z= 0.195
  Angle     :  0.524   8.478  11373  Z= 0.282
  Chirality :  0.042   0.235   1301
  Planarity :  0.003   0.045   1443
  Dihedral  :  4.681  45.074   1207
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  9.88 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.26), residues: 1025
  helix:  2.33 (0.25), residues: 413
  sheet:  1.21 (0.35), residues: 194
  loop : -0.15 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP R 275 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.015   0.002   PHE A 212 
 TYR   0.016   0.002   TYR B 105 
 ARG   0.006   0.000   ARG B 197 

*********************** 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: 27
    poor density    : 110
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6940 (mtmt) cc_final: 0.6359 (mmmt)
REVERT: A  223 ASP cc_start: 0.7939 (t0) cc_final: 0.7653 (t70)
REVERT: A  230 GLU cc_start: 0.8304 (mt-10) cc_final: 0.6352 (tt0)
REVERT: A  232 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8154 (ptp90)
REVERT: B   78 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8580 (tppt)
REVERT: B  197 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7189 (mmp80)
REVERT: B  217 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7442 (pp-130)
REVERT: B  259 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7465 (tt0)
REVERT: B  325 MET cc_start: 0.8474 (tpp) cc_final: 0.8256 (mmm)
REVERT: G   21 MET cc_start: 0.6409 (ttp) cc_final: 0.5464 (tmt)
REVERT: N   21 SER cc_start: 0.8699 (t) cc_final: 0.8492 (t)
REVERT: N   25 SER cc_start: 0.7527 (OUTLIER) cc_final: 0.7256 (p)
REVERT: N  110 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8264 (m)
REVERT: R  122 ASP cc_start: 0.8313 (p0) cc_final: 0.7837 (p0)
REVERT: R  201 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7885 (m)
  outliers start: 27
  outliers final: 10
  residues processed: 125
  average time/residue: 1.1286
  time to fit residues: 150.9815
Evaluate side-chains
  117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
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  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 32 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.185939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145022 restraints weight = 8458.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.00
r_work: 0.3505 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8388  Z= 0.247
  Angle     :  0.565  10.463  11373  Z= 0.300
  Chirality :  0.044   0.273   1301
  Planarity :  0.004   0.043   1443
  Dihedral  :  4.854  47.082   1207
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 11.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.26), residues: 1025
  helix:  2.47 (0.25), residues: 407
  sheet:  0.96 (0.35), residues: 202
  loop : -0.07 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 275 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.017   0.002   PHE N  68 
 TYR   0.018   0.002   TYR B 105 
 ARG   0.007   0.000   ARG A 317 

*********************** 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
  134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 100
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.6950 (mtmt) cc_final: 0.6358 (mmmt)
REVERT: A  229 ASP cc_start: 0.5549 (OUTLIER) cc_final: 0.5186 (p0)
REVERT: A  232 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8196 (ptp90)
REVERT: A  268 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6831 (mp0)
REVERT: B   59 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7747 (m-80)
REVERT: B   78 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8700 (tppt)
REVERT: B  217 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6206 (mmp)
REVERT: B  219 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6748 (mtm-85)
REVERT: B  268 ASN cc_start: 0.7477 (m-40) cc_final: 0.7181 (p0)
REVERT: B  325 MET cc_start: 0.8515 (tpp) cc_final: 0.8273 (mmm)
REVERT: G   21 MET cc_start: 0.6376 (ttp) cc_final: 0.5344 (tmt)
REVERT: N   25 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7452 (p)
REVERT: R  122 ASP cc_start: 0.8443 (p0) cc_final: 0.7923 (p0)
REVERT: R  171 THR cc_start: 0.6314 (OUTLIER) cc_final: 0.5966 (t)
  outliers start: 34
  outliers final: 14
  residues processed: 120
  average time/residue: 1.2210
  time to fit residues: 157.4035
Evaluate side-chains
  116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  232 ARG
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   76 ASP
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  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   25 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 97 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   overall best weight:    2.4988

-------------------------------------------------------------------------------
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 = 0.4083 r_free = 0.4083 target = 0.183212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.142625 restraints weight = 8411.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.82
r_work: 0.3460 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   8388  Z= 0.350
  Angle     :  0.641  13.012  11373  Z= 0.338
  Chirality :  0.046   0.318   1301
  Planarity :  0.004   0.046   1443
  Dihedral  :  5.299  47.171   1207
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 10.66 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1025
  helix:  2.32 (0.25), residues: 408
  sheet:  0.83 (0.34), residues: 212
  loop : -0.27 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R 275 
 HIS   0.007   0.002   HIS B 225 
 PHE   0.021   0.002   PHE N  68 
 TYR   0.019   0.002   TYR N 117 
 ARG   0.005   0.001   ARG A 317 

*********************** 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
  137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 98
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6929 (mtmt) cc_final: 0.6312 (mmmt)
REVERT: A  229 ASP cc_start: 0.5669 (OUTLIER) cc_final: 0.5390 (p0)
REVERT: A  230 GLU cc_start: 0.8465 (mt-10) cc_final: 0.6613 (tm-30)
REVERT: B   59 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7670 (m-80)
REVERT: B   78 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8763 (tppt)
REVERT: B   96 ARG cc_start: 0.7975 (mmt90) cc_final: 0.7642 (mtm-85)
REVERT: B  217 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6252 (mmp)
REVERT: B  219 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6697 (mtm-85)
REVERT: B  259 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7566 (tt0)
REVERT: G   21 MET cc_start: 0.6494 (ttp) cc_final: 0.5469 (tmt)
REVERT: R  122 ASP cc_start: 0.8468 (p0) cc_final: 0.7938 (p0)
REVERT: R  171 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.6037 (t)
  outliers start: 39
  outliers final: 21
  residues processed: 119
  average time/residue: 1.1253
  time to fit residues: 143.5666
Evaluate side-chains
  122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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  224 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   76 ASP
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  214 ARG
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   12 VAL
Chi-restraints excluded: chain N residue   28 THR
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  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 34 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.186282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.145366 restraints weight = 8427.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 1.98
r_work: 0.3497 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8388  Z= 0.197
  Angle     :  0.536  14.259  11373  Z= 0.283
  Chirality :  0.042   0.248   1301
  Planarity :  0.003   0.045   1443
  Dihedral  :  4.948  49.218   1207
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 11.78 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.26), residues: 1025
  helix:  2.59 (0.25), residues: 408
  sheet:  0.96 (0.34), residues: 208
  loop : -0.23 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.016   0.002   PHE A 212 
 TYR   0.010   0.001   TYR N  80 
 ARG   0.004   0.000   ARG A 317 

*********************** 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
  130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6919 (mtmt) cc_final: 0.6290 (mmmt)
REVERT: A  230 GLU cc_start: 0.8473 (mt-10) cc_final: 0.6675 (tm-30)
REVERT: B   59 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7687 (m-80)
REVERT: B   96 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7589 (mtm-85)
REVERT: B  153 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7505 (p0)
REVERT: B  217 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7283 (ppp)
REVERT: B  219 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6763 (mtm-85)
REVERT: B  259 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7580 (tt0)
REVERT: G   21 MET cc_start: 0.6528 (ttp) cc_final: 0.5545 (tmt)
REVERT: N    3 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6960 (pp30)
REVERT: R  122 ASP cc_start: 0.8407 (p0) cc_final: 0.7885 (p0)
REVERT: R  142 ILE cc_start: 0.7484 (mt) cc_final: 0.7269 (mp)
REVERT: R  171 THR cc_start: 0.6393 (OUTLIER) cc_final: 0.6013 (t)
  outliers start: 32
  outliers final: 19
  residues processed: 114
  average time/residue: 1.1008
  time to fit residues: 135.1091
Evaluate side-chains
  119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  239 ASN
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  195 ASP
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    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue  141 LEU
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  178 VAL
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 96 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.3980
   chunk 35 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.188206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.146906 restraints weight = 8447.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.90
r_work: 0.3528 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8388  Z= 0.155
  Angle     :  0.505  14.788  11373  Z= 0.263
  Chirality :  0.042   0.316   1301
  Planarity :  0.003   0.044   1443
  Dihedral  :  4.691  48.430   1207
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 12.23 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.26), residues: 1025
  helix:  2.68 (0.25), residues: 411
  sheet:  0.86 (0.35), residues: 212
  loop : -0.13 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.012   0.001   TYR N  80 
 ARG   0.005   0.000   ARG A 317 

*********************** 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
  129 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5680 (p0)
REVERT: A  230 GLU cc_start: 0.8454 (mt-10) cc_final: 0.6518 (tm-30)
REVERT: A  342 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7658 (ttp-170)
REVERT: B   45 MET cc_start: 0.8506 (mtt) cc_final: 0.8090 (mtt)
REVERT: B   59 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7685 (m-80)
REVERT: B   96 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7619 (mtm-85)
REVERT: B  153 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7445 (p0)
REVERT: B  217 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7338 (ppp)
REVERT: B  259 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7513 (tt0)
REVERT: B  325 MET cc_start: 0.8501 (tpp) cc_final: 0.8258 (mmm)
REVERT: G   21 MET cc_start: 0.6424 (ttp) cc_final: 0.5489 (tmt)
REVERT: N    3 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6963 (pp30)
REVERT: R  122 ASP cc_start: 0.8337 (p0) cc_final: 0.7842 (p0)
REVERT: R  171 THR cc_start: 0.6348 (OUTLIER) cc_final: 0.5959 (t)
  outliers start: 30
  outliers final: 13
  residues processed: 114
  average time/residue: 1.0561
  time to fit residues: 129.3643
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  : 0.940 
-------------------------------------------------------------------------------
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  342 ARG
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   71 SER
Chi-restraints excluded: chain R residue  141 LEU
Chi-restraints excluded: chain R residue  171 THR
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 81 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 1 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.4110 r_free = 0.4110 target = 0.186178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.145911 restraints weight = 8533.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.04
r_work: 0.3496 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8388  Z= 0.207
  Angle     :  0.536  14.203  11373  Z= 0.281
  Chirality :  0.043   0.300   1301
  Planarity :  0.003   0.044   1443
  Dihedral  :  4.828  47.304   1207
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 12.57 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.26), residues: 1025
  helix:  2.65 (0.25), residues: 414
  sheet:  0.85 (0.34), residues: 216
  loop : -0.24 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.014   0.002   PHE A 212 
 TYR   0.013   0.002   TYR N  80 
 ARG   0.004   0.000   ARG A 317 

*********************** 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
  127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6973 (mtmt) cc_final: 0.6309 (mmmt)
REVERT: A  229 ASP cc_start: 0.5944 (OUTLIER) cc_final: 0.5639 (p0)
REVERT: A  230 GLU cc_start: 0.8485 (mt-10) cc_final: 0.6542 (tm-30)
REVERT: A  342 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7739 (ttp-170)
REVERT: B   59 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7721 (m-80)
REVERT: B   96 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7663 (mtm-85)
REVERT: B  153 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7540 (p0)
REVERT: B  217 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7360 (ppp)
REVERT: B  259 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7551 (tt0)
REVERT: B  267 ASP cc_start: 0.8336 (m-30) cc_final: 0.8016 (m-30)
REVERT: G   21 MET cc_start: 0.6373 (ttp) cc_final: 0.5475 (tmt)
REVERT: N    3 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7041 (pp30)
REVERT: R  122 ASP cc_start: 0.8365 (p0) cc_final: 0.7861 (p0)
REVERT: R  171 THR cc_start: 0.6275 (OUTLIER) cc_final: 0.5898 (t)
  outliers start: 30
  outliers final: 16
  residues processed: 114
  average time/residue: 1.1246
  time to fit residues: 137.4537
Evaluate side-chains
  118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
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  342 ARG
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  153 ASP
Chi-restraints excluded: chain B residue  195 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 R residue  141 LEU
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  178 VAL
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 80 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0770
   chunk 86 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0050
   chunk 90 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0970
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.3750

-------------------------------------------------------------------------------
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 = 0.4160 r_free = 0.4160 target = 0.191205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.150671 restraints weight = 8606.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.96
r_work: 0.3574 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8388  Z= 0.119
  Angle     :  0.478  15.822  11373  Z= 0.246
  Chirality :  0.041   0.330   1301
  Planarity :  0.003   0.043   1443
  Dihedral  :  4.438  46.461   1207
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.25 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.26), residues: 1025
  helix:  2.85 (0.25), residues: 411
  sheet:  0.92 (0.34), residues: 216
  loop : -0.11 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.012   0.001   TYR N  80 
 ARG   0.003   0.000   ARG A 317 

*********************** 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
  119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7707 (m-80)
REVERT: B   96 ARG cc_start: 0.7890 (mmt90) cc_final: 0.7630 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7991 (tt0) cc_final: 0.7383 (tt0)
REVERT: B  267 ASP cc_start: 0.8190 (m-30) cc_final: 0.7963 (m-30)
REVERT: B  325 MET cc_start: 0.8461 (tpp) cc_final: 0.8235 (mmm)
REVERT: G   21 MET cc_start: 0.6341 (ttp) cc_final: 0.5405 (tmt)
REVERT: N    3 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7018 (pp30)
REVERT: R  122 ASP cc_start: 0.8277 (p0) cc_final: 0.7841 (p0)
  outliers start: 16
  outliers final: 7
  residues processed: 112
  average time/residue: 0.9885
  time to fit residues: 119.6281
Evaluate side-chains
  103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain B residue   59 TYR
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   71 SER
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  178 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    2.5786

-------------------------------------------------------------------------------
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 = 0.4079 r_free = 0.4079 target = 0.183006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.142004 restraints weight = 8422.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 1.85
r_work: 0.3454 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8388  Z= 0.356
  Angle     :  0.636  14.469  11373  Z= 0.332
  Chirality :  0.046   0.340   1301
  Planarity :  0.004   0.044   1443
  Dihedral  :  5.170  44.860   1207
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.59 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.26), residues: 1025
  helix:  2.57 (0.25), residues: 409
  sheet:  0.81 (0.34), residues: 216
  loop : -0.31 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP R 275 
 HIS   0.008   0.002   HIS B 225 
 PHE   0.025   0.002   PHE B 241 
 TYR   0.016   0.002   TYR N 117 
 ARG   0.003   0.000   ARG A 317 

********************** 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
  122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6943 (mtmt) cc_final: 0.6310 (mmmt)
REVERT: A  230 GLU cc_start: 0.8499 (mt-10) cc_final: 0.6571 (tm-30)
REVERT: A  342 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7670 (ttp-170)
REVERT: B   59 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7671 (m-80)
REVERT: B   96 ARG cc_start: 0.7990 (mmt90) cc_final: 0.7702 (mtm-85)
REVERT: B  267 ASP cc_start: 0.8252 (m-30) cc_final: 0.7945 (m-30)
REVERT: G   21 MET cc_start: 0.6520 (ttp) cc_final: 0.5491 (tmt)
REVERT: N    3 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7017 (pp30)
REVERT: R  122 ASP cc_start: 0.8371 (p0) cc_final: 0.7848 (p0)
REVERT: R  160 SER cc_start: 0.8084 (m) cc_final: 0.7586 (p)
REVERT: R  171 THR cc_start: 0.6230 (OUTLIER) cc_final: 0.5858 (t)
  outliers start: 19
  outliers final: 13
  residues processed: 112
  average time/residue: 1.0539
  time to fit residues: 126.8858
Evaluate side-chains
  117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  342 ARG
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  205 ASP
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   28 THR
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue  141 LEU
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  178 VAL
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 14 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0370
   chunk 94 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.2064

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.186152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144939 restraints weight = 8553.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.97
r_work: 0.3504 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8388  Z= 0.204
  Angle     :  0.545  14.396  11373  Z= 0.285
  Chirality :  0.043   0.321   1301
  Planarity :  0.003   0.043   1443
  Dihedral  :  4.856  46.466   1207
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.81 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1025
  helix:  2.59 (0.25), residues: 414
  sheet:  0.79 (0.34), residues: 216
  loop : -0.31 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.016   0.002   PHE N  68 
 TYR   0.012   0.001   TYR N  80 
 ARG   0.003   0.000   ARG A 317 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 6860.68 seconds
wall clock time: 118 minutes 50.73 seconds (7130.73 seconds total)