Starting phenix.real_space_refine
on Fri Jul 25 20:24:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yut_39582/07_2025/8yut_39582.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yut_39582/07_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_39582/07_2025/8yut_39582.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yut_39582/07_2025/8yut_39582.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yut_39582/07_2025/8yut_39582.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yut_39582/07_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-5711/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: 4.85, per 1000 atoms: 0.59
  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: 2.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.83
  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: 2.58

  Time building geometry restraints manager: 2.66 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:             0.450
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.190
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:15.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.810
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.885 
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: 1.1734
  time to fit residues: 202.2730
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  : 0.862 
-------------------------------------------------------------------------------
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   8391  Z= 0.133
  Angle     :  0.538   9.666  11379  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04903 (  438)
  hydrogen bonds       : angle       4.81707 ( 1248)
  SS BOND              : bond        0.00383 (    3)
  SS BOND              : angle       0.37860 (    6)
  covalent geometry    : bond        0.00280 ( 8388)
  covalent geometry    : angle       0.53789 (11373)

*********************** 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  : 0.892 
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: 1.1967
  time to fit residues: 160.7148
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  : 0.913 
-------------------------------------------------------------------------------
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   8391  Z= 0.132
  Angle     :  0.524   8.478  11379  Z= 0.281
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04688 (  438)
  hydrogen bonds       : angle       4.61489 ( 1248)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       0.32234 (    6)
  covalent geometry    : bond        0.00292 ( 8388)
  covalent geometry    : angle       0.52413 (11373)

*********************** 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  : 0.909 
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: 1.1591
  time to fit residues: 155.7972
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  : 0.959 
-------------------------------------------------------------------------------
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:    5.9990
   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:    2.3986

-------------------------------------------------------------------------------
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 = 0.4072 r_free = 0.4072 target = 0.182433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.142276 restraints weight = 8484.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.00
r_work: 0.3471 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8391  Z= 0.218
  Angle     :  0.636   8.951  11379  Z= 0.337
  Chirality :  0.046   0.278   1301
  Planarity :  0.005   0.045   1443
  Dihedral  :  5.178  46.716   1207
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 11.34 %
    Favored  : 84.74 %
  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:  1.44 (0.25), residues: 1025
  helix:  2.24 (0.25), residues: 407
  sheet:  0.84 (0.34), residues: 212
  loop : -0.29 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 275 
 HIS   0.009   0.002   HIS A 357 
 PHE   0.021   0.002   PHE N  68 
 TYR   0.020   0.002   TYR B 105 
 ARG   0.009   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05729 (  438)
  hydrogen bonds       : angle       4.88843 ( 1248)
  SS BOND              : bond        0.00599 (    3)
  SS BOND              : angle       2.65607 (    6)
  covalent geometry    : bond        0.00517 ( 8388)
  covalent geometry    : angle       0.63329 (11373)

*********************** 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
  138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.6927 (mtmt) cc_final: 0.6327 (mmmt)
REVERT: A  229 ASP cc_start: 0.5590 (OUTLIER) cc_final: 0.5258 (p0)
REVERT: A  230 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8109 (mt-10)
REVERT: A  268 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6771 (mp0)
REVERT: B   59 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7672 (m-80)
REVERT: B   78 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8741 (tppt)
REVERT: B  217 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6183 (mmt)
REVERT: B  219 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6790 (mtm-85)
REVERT: B  259 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7891 (tt0)
REVERT: G   21 MET cc_start: 0.6543 (ttp) cc_final: 0.5474 (tmt)
REVERT: R  122 ASP cc_start: 0.8477 (p0) cc_final: 0.7956 (p0)
REVERT: R  160 SER cc_start: 0.8010 (t) cc_final: 0.7764 (p)
REVERT: R  171 THR cc_start: 0.6415 (OUTLIER) cc_final: 0.6023 (t)
  outliers start: 35
  outliers final: 13
  residues processed: 122
  average time/residue: 1.0623
  time to fit residues: 139.0564
Evaluate side-chains
  115 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
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  234 TRP
Chi-restraints excluded: chain A residue  268 GLU
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  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   46 GLU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0370
   chunk 14 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.3864

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.185621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145131 restraints weight = 8440.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.04
r_work: 0.3506 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8391  Z= 0.152
  Angle     :  0.569  12.856  11379  Z= 0.301
  Chirality :  0.043   0.301   1301
  Planarity :  0.004   0.045   1443
  Dihedral  :  5.049  48.903   1207
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.22 %
    Favored  : 85.07 %
  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:  1.62 (0.26), residues: 1025
  helix:  2.46 (0.25), residues: 408
  sheet:  0.87 (0.34), residues: 210
  loop : -0.23 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.016   0.002   PHE A 212 
 TYR   0.013   0.002   TYR B 105 
 ARG   0.005   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04834 (  438)
  hydrogen bonds       : angle       4.62574 ( 1248)
  SS BOND              : bond        0.01175 (    3)
  SS BOND              : angle       4.13684 (    6)
  covalent geometry    : bond        0.00347 ( 8388)
  covalent geometry    : angle       0.56117 (11373)

*********************** 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
  132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 1.783 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.6945 (mtmt) cc_final: 0.6336 (mmmt)
REVERT: A  230 GLU cc_start: 0.8402 (mt-10) cc_final: 0.6505 (tm-30)
REVERT: A  268 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6869 (tp30)
REVERT: B   59 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7688 (m-80)
REVERT: B   96 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7751 (mtm-85)
REVERT: B  153 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7591 (p0)
REVERT: B  217 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7234 (ppp)
REVERT: B  219 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6772 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7397 (tt0)
REVERT: B  325 MET cc_start: 0.8580 (tpp) cc_final: 0.8356 (mmm)
REVERT: G   21 MET cc_start: 0.6542 (ttp) cc_final: 0.5564 (tmt)
REVERT: R  122 ASP cc_start: 0.8442 (p0) cc_final: 0.7917 (p0)
REVERT: R  160 SER cc_start: 0.8055 (t) cc_final: 0.7784 (p)
REVERT: R  171 THR cc_start: 0.6382 (OUTLIER) cc_final: 0.5999 (t)
  outliers start: 33
  outliers final: 17
  residues processed: 116
  average time/residue: 1.6631
  time to fit residues: 206.0937
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  : 2.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  239 ASN
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  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    7 SER
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   64 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0370
   chunk 24 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7258

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.188648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.147178 restraints weight = 8450.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.91
r_work: 0.3531 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8391  Z= 0.109
  Angle     :  0.505  14.532  11379  Z= 0.265
  Chirality :  0.041   0.232   1301
  Planarity :  0.003   0.043   1443
  Dihedral  :  4.709  48.774   1207
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.23 %
    Favored  : 84.62 %
  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:  1.79 (0.26), residues: 1025
  helix:  2.63 (0.25), residues: 410
  sheet:  0.89 (0.35), residues: 212
  loop : -0.14 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.014   0.001   TYR N  80 
 ARG   0.004   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  438)
  hydrogen bonds       : angle       4.36491 ( 1248)
  SS BOND              : bond        0.00522 (    3)
  SS BOND              : angle       3.47509 (    6)
  covalent geometry    : bond        0.00235 ( 8388)
  covalent geometry    : angle       0.49841 (11373)

*********************** 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
  127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.5515 (p0)
REVERT: A  230 GLU cc_start: 0.8370 (mt-10) cc_final: 0.6437 (tm-30)
REVERT: B   45 MET cc_start: 0.8496 (mtt) cc_final: 0.8094 (mtt)
REVERT: B   59 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7700 (m-80)
REVERT: B   96 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7751 (mtm-85)
REVERT: B  217 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7420 (ppp)
REVERT: B  259 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7411 (tt0)
REVERT: G   21 MET cc_start: 0.6467 (ttp) cc_final: 0.5507 (tmt)
REVERT: N    3 GLN cc_start: 0.7403 (pt0) cc_final: 0.6980 (pp30)
REVERT: R  122 ASP cc_start: 0.8372 (p0) cc_final: 0.7879 (p0)
REVERT: R  160 SER cc_start: 0.8018 (t) cc_final: 0.7760 (p)
REVERT: R  171 THR cc_start: 0.6397 (OUTLIER) cc_final: 0.6006 (t)
  outliers start: 28
  outliers final: 12
  residues processed: 113
  average time/residue: 1.0282
  time to fit residues: 125.2274
Evaluate side-chains
  109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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  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  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   28 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0870
   chunk 60 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.7564

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.185717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145657 restraints weight = 8421.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 1.89
r_work: 0.3498 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8391  Z= 0.169
  Angle     :  0.581  13.905  11379  Z= 0.304
  Chirality :  0.044   0.332   1301
  Planarity :  0.004   0.043   1443
  Dihedral  :  5.016  47.725   1207
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 12.46 %
    Favored  : 84.18 %
  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:  1.70 (0.26), residues: 1025
  helix:  2.59 (0.25), residues: 409
  sheet:  0.91 (0.34), residues: 209
  loop : -0.28 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.015   0.002   PHE N  68 
 TYR   0.014   0.002   TYR B 105 
 ARG   0.004   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04952 (  438)
  hydrogen bonds       : angle       4.61647 ( 1248)
  SS BOND              : bond        0.00577 (    3)
  SS BOND              : angle       4.04180 (    6)
  covalent geometry    : bond        0.00396 ( 8388)
  covalent geometry    : angle       0.57324 (11373)

*********************** 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
  128 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6954 (mtmt) cc_final: 0.6314 (mmmt)
REVERT: A  229 ASP cc_start: 0.5844 (OUTLIER) cc_final: 0.5545 (p0)
REVERT: A  230 GLU cc_start: 0.8373 (mt-10) cc_final: 0.6449 (tm-30)
REVERT: A  342 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7708 (ttp-170)
REVERT: B   59 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7677 (m-80)
REVERT: B   96 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7709 (mtm-85)
REVERT: B  217 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7341 (ppp)
REVERT: B  259 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7482 (tt0)
REVERT: B  268 ASN cc_start: 0.8340 (p0) cc_final: 0.8070 (p0)
REVERT: G   21 MET cc_start: 0.6532 (ttp) cc_final: 0.5595 (tmt)
REVERT: N    3 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7051 (pp30)
REVERT: R  122 ASP cc_start: 0.8402 (p0) cc_final: 0.7884 (p0)
REVERT: R  160 SER cc_start: 0.8120 (t) cc_final: 0.7838 (p)
REVERT: R  171 THR cc_start: 0.6352 (OUTLIER) cc_final: 0.5971 (t)
  outliers start: 30
  outliers final: 18
  residues processed: 114
  average time/residue: 1.0874
  time to fit residues: 132.9993
Evaluate side-chains
  122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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   76 ASP
Chi-restraints excluded: chain B residue   87 THR
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   64 VAL
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:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 57 optimal weight:   30.0000
   chunk 1 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.186575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.146022 restraints weight = 8527.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.00
r_work: 0.3514 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8391  Z= 0.126
  Angle     :  0.529  14.553  11379  Z= 0.277
  Chirality :  0.042   0.293   1301
  Planarity :  0.003   0.043   1443
  Dihedral  :  4.815  48.334   1207
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.91 %
    Favored  : 84.18 %
  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:  1.73 (0.26), residues: 1025
  helix:  2.61 (0.25), residues: 415
  sheet:  0.80 (0.34), residues: 217
  loop : -0.24 (0.30), residues: 393

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   0.015   0.002   PHE A 212 
 TYR   0.013   0.001   TYR N  80 
 ARG   0.004   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04410 (  438)
  hydrogen bonds       : angle       4.45068 ( 1248)
  SS BOND              : bond        0.00437 (    3)
  SS BOND              : angle       3.35015 (    6)
  covalent geometry    : bond        0.00284 ( 8388)
  covalent geometry    : angle       0.52307 (11373)

*********************** 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: 26
    poor density    : 101
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6940 (mtmt) cc_final: 0.6276 (mmmt)
REVERT: A  229 ASP cc_start: 0.5954 (OUTLIER) cc_final: 0.5602 (p0)
REVERT: A  230 GLU cc_start: 0.8372 (mt-10) cc_final: 0.6449 (tm-30)
REVERT: A  342 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7679 (ttp-170)
REVERT: B   59 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7660 (m-80)
REVERT: B   96 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7734 (mtm-85)
REVERT: B  153 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7538 (p0)
REVERT: B  217 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7323 (ppp)
REVERT: B  267 ASP cc_start: 0.8365 (m-30) cc_final: 0.8052 (m-30)
REVERT: B  325 MET cc_start: 0.8535 (tpp) cc_final: 0.8273 (mmm)
REVERT: G   21 MET cc_start: 0.6449 (ttp) cc_final: 0.5577 (tmt)
REVERT: N    3 GLN cc_start: 0.7333 (pt0) cc_final: 0.6982 (pp30)
REVERT: R  122 ASP cc_start: 0.8314 (p0) cc_final: 0.7806 (p0)
REVERT: R  160 SER cc_start: 0.8092 (t) cc_final: 0.7793 (p)
REVERT: R  171 THR cc_start: 0.6253 (OUTLIER) cc_final: 0.5891 (t)
  outliers start: 26
  outliers final: 17
  residues processed: 114
  average time/residue: 1.1321
  time to fit residues: 138.3142
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  : 0.827 
-------------------------------------------------------------------------------
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   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  247 ASP
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0470
   chunk 86 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0770
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.8242

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.187846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.147109 restraints weight = 8549.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.97
r_work: 0.3528 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8391  Z= 0.112
  Angle     :  0.512  14.819  11379  Z= 0.266
  Chirality :  0.042   0.336   1301
  Planarity :  0.003   0.042   1443
  Dihedral  :  4.658  46.951   1207
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.13 %
    Favored  : 84.18 %
  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:  1.84 (0.26), residues: 1025
  helix:  2.78 (0.25), residues: 410
  sheet:  0.85 (0.34), residues: 216
  loop : -0.22 (0.30), residues: 399

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  438)
  hydrogen bonds       : angle       4.34319 ( 1248)
  SS BOND              : bond        0.00414 (    3)
  SS BOND              : angle       2.99076 (    6)
  covalent geometry    : bond        0.00244 ( 8388)
  covalent geometry    : angle       0.50794 (11373)

*********************** 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
  121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5605 (p0)
REVERT: A  230 GLU cc_start: 0.8382 (mt-10) cc_final: 0.6465 (tm-30)
REVERT: B   59 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7710 (m-80)
REVERT: B  153 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7473 (p0)
REVERT: B  217 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7331 (ppp)
REVERT: B  267 ASP cc_start: 0.8296 (m-30) cc_final: 0.7998 (m-30)
REVERT: B  325 MET cc_start: 0.8532 (tpp) cc_final: 0.8281 (mmm)
REVERT: G   21 MET cc_start: 0.6243 (ttp) cc_final: 0.5330 (tmt)
REVERT: N    3 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6983 (pp30)
REVERT: R  122 ASP cc_start: 0.8320 (p0) cc_final: 0.7812 (p0)
REVERT: R  160 SER cc_start: 0.8078 (t) cc_final: 0.7781 (p)
REVERT: R  171 THR cc_start: 0.6251 (OUTLIER) cc_final: 0.5835 (t)
  outliers start: 24
  outliers final: 14
  residues processed: 108
  average time/residue: 1.0657
  time to fit residues: 123.6598
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  : 0.897 
-------------------------------------------------------------------------------
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  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  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    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 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 98 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 92 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4095 r_free = 0.4095 target = 0.184586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.144150 restraints weight = 8416.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.00
r_work: 0.3470 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8391  Z= 0.171
  Angle     :  0.582  13.948  11379  Z= 0.304
  Chirality :  0.044   0.332   1301
  Planarity :  0.004   0.042   1443
  Dihedral  :  4.976  46.156   1207
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.02 %
    Favored  : 84.18 %
  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:  1.75 (0.26), residues: 1025
  helix:  2.70 (0.25), residues: 409
  sheet:  0.79 (0.34), residues: 216
  loop : -0.27 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP R 275 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.017   0.002   PHE N  68 
 TYR   0.015   0.002   TYR N  80 
 ARG   0.004   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04950 (  438)
  hydrogen bonds       : angle       4.59480 ( 1248)
  SS BOND              : bond        0.00444 (    3)
  SS BOND              : angle       3.80822 (    6)
  covalent geometry    : bond        0.00400 ( 8388)
  covalent geometry    : angle       0.57568 (11373)

********************** 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
  126 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6998 (mtmt) cc_final: 0.6355 (mmmt)
REVERT: A  229 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5532 (p0)
REVERT: A  230 GLU cc_start: 0.8356 (mt-10) cc_final: 0.6441 (tm-30)
REVERT: A  342 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7725 (ttp-170)
REVERT: B   59 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7657 (m-80)
REVERT: B  153 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7603 (p0)
REVERT: B  217 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.6282 (mmp)
REVERT: B  267 ASP cc_start: 0.8317 (m-30) cc_final: 0.8008 (m-30)
REVERT: G   21 MET cc_start: 0.6400 (ttp) cc_final: 0.5472 (tmt)
REVERT: N    3 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7007 (pp30)
REVERT: R  122 ASP cc_start: 0.8380 (p0) cc_final: 0.7864 (p0)
REVERT: R  160 SER cc_start: 0.8116 (t) cc_final: 0.7782 (p)
REVERT: R  171 THR cc_start: 0.6203 (OUTLIER) cc_final: 0.5856 (t)
  outliers start: 25
  outliers final: 16
  residues processed: 115
  average time/residue: 1.0405
  time to fit residues: 128.6891
Evaluate side-chains
  120 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
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  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    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   52 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
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:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0980
   chunk 32 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 96 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.188025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148142 restraints weight = 8563.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.05
r_work: 0.3534 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8391  Z= 0.110
  Angle     :  0.510  14.923  11379  Z= 0.264
  Chirality :  0.042   0.314   1301
  Planarity :  0.003   0.042   1443
  Dihedral  :  4.656  46.252   1207
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.24 %
    Favored  : 84.18 %
  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:  1.86 (0.26), residues: 1025
  helix:  2.79 (0.25), residues: 411
  sheet:  0.84 (0.34), residues: 216
  loop : -0.20 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   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   0.004   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  438)
  hydrogen bonds       : angle       4.31848 ( 1248)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       2.83881 (    6)
  covalent geometry    : bond        0.00240 ( 8388)
  covalent geometry    : angle       0.50638 (11373)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

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Job complete
usr+sys time: 6947.25 seconds
wall clock time: 122 minutes 20.05 seconds (7340.05 seconds total)