Starting phenix.real_space_refine
on Sun Apr 27 22:40:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6v_50241/04_2025/9f6v_50241.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6v_50241/04_2025/9f6v_50241.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6v_50241/04_2025/9f6v_50241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6v_50241/04_2025/9f6v_50241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6v_50241/04_2025/9f6v_50241.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6v_50241/04_2025/9f6v_50241.cif"
  }
  resolution = 3.5
  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=  -0.004 sd=   0.172
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      34      5.16       5
     C    4206      2.51       5
     N    1093      2.21       5
     O    1274      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6610
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3230
          Classifications: {'peptide': 422}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406}
    Chain: "D"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3348
          Classifications: {'peptide': 422}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 405}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.42, per 1000 atoms: 0.67
  Number of scatterers: 6610
  At special positions: 0
  Unit cell: (98.8, 75.4, 104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       3     15.00
     O    1274      8.00
     N    1093      7.00
     C    4206      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.81
  Conformation dependent library (CDL) restraints added in 982.8 milliseconds
  

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      52.1% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 29
    Processing helix  chain 'A' and resid 44 through 47
    Processing helix  chain 'A' and resid 66 through 72
      removed outlier: 3.622A  pdb=" N   VAL A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'A' and resid 78 through 81
    Processing helix  chain 'A' and resid 82 through 84
      No H-bonds generated for 'chain 'A' and resid 82 through 84'
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 105 through 122
    Processing helix  chain 'A' and resid 138 through 155
      removed outlier: 3.715A  pdb=" N   GLY A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 192
      removed outlier: 3.603A  pdb=" N   ASN A 180 " --> pdb=" O   VAL A 176 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 217 through 234
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 245 through 254
    Processing helix  chain 'A' and resid 281 through 290
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 318 through 333
    Processing helix  chain 'A' and resid 368 through 384
      removed outlier: 4.271A  pdb=" N   PHE A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 395
      removed outlier: 3.822A  pdb=" N   PHE A 392 " --> pdb=" O   PHE A 388 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER A 395 " --> pdb=" O   TRP A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 420
    Processing helix  chain 'D' and resid 11 through 29
      Proline residue:  D  19  - end of helix
    Processing helix  chain 'D' and resid 44 through 47
    Processing helix  chain 'D' and resid 68 through 77
    Processing helix  chain 'D' and resid 84 through 86
      No H-bonds generated for 'chain 'D' and resid 84 through 86'
    Processing helix  chain 'D' and resid 98 through 104
      removed outlier: 3.999A  pdb=" N   GLY D 102 " --> pdb=" O   LEU D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 109
    Processing helix  chain 'D' and resid 110 through 123
    Processing helix  chain 'D' and resid 139 through 155
      Proline residue:  D 147  - end of helix
    Processing helix  chain 'D' and resid 178 through 191
      removed outlier: 3.869A  pdb=" N   LYS D 189 " --> pdb=" O   LEU D 185 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 212
    Processing helix  chain 'D' and resid 214 through 218
    Processing helix  chain 'D' and resid 219 through 237
      removed outlier: 4.296A  pdb=" N   THR D 237 " --> pdb=" O   GLU D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 256
    Processing helix  chain 'D' and resid 272 through 276
    Processing helix  chain 'D' and resid 283 through 293
    Processing helix  chain 'D' and resid 294 through 297
    Processing helix  chain 'D' and resid 320 through 328
    Processing helix  chain 'D' and resid 329 through 332
    Processing helix  chain 'D' and resid 369 through 386
      removed outlier: 3.774A  pdb=" N   LEU D 373 " --> pdb=" O   GLY D 369 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 396
    Processing helix  chain 'D' and resid 401 through 421
      removed outlier: 3.700A  pdb=" N   ASP D 421 " --> pdb=" O   GLU D 417 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 8.345A  pdb=" N   VAL A  87 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL A  62 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   GLU A   4 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   PHE A 129 " --> pdb=" O   GLU A   4 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL A   6 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   LEU A 131 " --> pdb=" O   VAL A   6 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ILE A   8 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   HIS A 133 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   VAL A  10 " --> pdb=" O   HIS A 133 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   PHE A 161 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   PHE A 129 " --> pdb=" O   PHE A 161 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   PHE A 163 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LEU A 131 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   ILE A 165 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   HIS A 133 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   ILE A 160 " --> pdb=" O   CYS A 194 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   ILE A 196 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   THR A 162 " --> pdb=" O   ILE A 196 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   LEU A 198 " --> pdb=" O   THR A 162 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   SER A 164 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   SER A 195 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   ALA A 264 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   VAL A 197 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 10.378A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 13.038A  pdb=" N   ASP A 199 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   PHE A 261 " --> pdb=" O   ASN A 365 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   ASN A 365 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A 308 " --> pdb=" O   ASN A 364 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52
    Processing sheet with id=AA3, first strand: chain 'D' and resid 88 through 90
      removed outlier: 8.178A  pdb=" N   VAL D  89 " --> pdb=" O   THR D  61 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU D  63 " --> pdb=" O   VAL D  89 " (cutoff:3.500A)
      removed outlier: 8.713A  pdb=" N   ILE D  62 " --> pdb=" O   VAL D   5 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   THR D   7 " --> pdb=" O   ILE D  62 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   VAL D  64 " --> pdb=" O   THR D   7 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   HIS D   9 " --> pdb=" O   VAL D  64 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   GLU D   4 " --> pdb=" O   GLN D 129 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   PHE D 131 " --> pdb=" O   GLU D   4 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ILE D   6 " --> pdb=" O   PHE D 131 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   VAL D 133 " --> pdb=" O   ILE D   6 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ILE D   8 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   HIS D 135 " --> pdb=" O   ILE D   8 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   VAL D  10 " --> pdb=" O   HIS D 135 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   GLN D 129 " --> pdb=" O   VAL D 161 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   MET D 163 " --> pdb=" O   GLN D 129 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   PHE D 131 " --> pdb=" O   MET D 163 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   TYR D 165 " --> pdb=" O   PHE D 131 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL D 133 " --> pdb=" O   TYR D 165 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   ILE D 167 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   HIS D 135 " --> pdb=" O   ILE D 167 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   SER D 197 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   THR D 266 " --> pdb=" O   SER D 197 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   ILE D 199 " --> pdb=" O   THR D 266 " (cutoff:3.500A)
      removed outlier: 10.437A  pdb=" N   MET D 268 " --> pdb=" O   ILE D 199 " (cutoff:3.500A)
      removed outlier: 12.549A  pdb=" N   ASP D 201 " --> pdb=" O   MET D 268 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   PHE D 263 " --> pdb=" O   HIS D 367 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   HIS D 367 " --> pdb=" O   PHE D 263 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 31 through 32
      removed outlier: 4.318A  pdb=" N   GLN D  36 " --> pdb=" O   ASP D  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 51

    325 hydrogen bonds defined for protein.
    930 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 2.12 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: 2128
        1.33 -     1.45: 1293
        1.45 -     1.57: 3255
        1.57 -     1.69: 5
        1.69 -     1.81: 58
  Bond restraints: 6739
  Sorted by residual:
  bond pdb=" CB  ASN A 364 "
       pdb=" CG  ASN A 364 "
    ideal  model  delta    sigma   weight residual
    1.516  1.338  0.178 2.50e-02 1.60e+03 5.08e+01
  bond pdb=" CB  TRP A 338 "
       pdb=" CG  TRP A 338 "
    ideal  model  delta    sigma   weight residual
    1.498  1.290  0.208 3.10e-02 1.04e+03 4.50e+01
  bond pdb=" CA  TRP A 391 "
       pdb=" C   TRP A 391 "
    ideal  model  delta    sigma   weight residual
    1.524  1.463  0.062 1.24e-02 6.50e+03 2.46e+01
  bond pdb=" CG  TRP A 338 "
       pdb=" CD2 TRP A 338 "
    ideal  model  delta    sigma   weight residual
    1.433  1.345  0.088 1.80e-02 3.09e+03 2.37e+01
  bond pdb=" CA  TRP A 338 "
       pdb=" C   TRP A 338 "
    ideal  model  delta    sigma   weight residual
    1.522  1.457  0.066 1.36e-02 5.41e+03 2.34e+01
  ... (remaining 6734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 8466
        2.76 -     5.52: 593
        5.52 -     8.28: 53
        8.28 -    11.04: 7
       11.04 -    13.80: 4
  Bond angle restraints: 9123
  Sorted by residual:
  angle pdb=" N   TRP A 391 "
        pdb=" CA  TRP A 391 "
        pdb=" C   TRP A 391 "
      ideal   model   delta    sigma   weight residual
     110.97  103.74    7.23 1.09e+00 8.42e-01 4.40e+01
  angle pdb=" C   SER A 239 "
        pdb=" CA  SER A 239 "
        pdb=" CB  SER A 239 "
      ideal   model   delta    sigma   weight residual
     116.63  109.07    7.56 1.16e+00 7.43e-01 4.25e+01
  angle pdb=" C   ALA D 183 "
        pdb=" N   ILE D 184 "
        pdb=" CA  ILE D 184 "
      ideal   model   delta    sigma   weight residual
     121.02  111.65    9.37 1.51e+00 4.39e-01 3.85e+01
  angle pdb=" C   ASP A  82 "
        pdb=" N   PRO A  83 "
        pdb=" CA  PRO A  83 "
      ideal   model   delta    sigma   weight residual
     119.56  125.26   -5.70 1.02e+00 9.61e-01 3.12e+01
  angle pdb=" C   THR D  61 "
        pdb=" CA  THR D  61 "
        pdb=" CB  THR D  61 "
      ideal   model   delta    sigma   weight residual
     109.79   98.35   11.44 2.05e+00 2.38e-01 3.11e+01
  ... (remaining 9118 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.92: 4006
       35.92 -    71.84: 43
       71.84 -   107.76: 3
      107.76 -   143.68: 3
      143.68 -   179.61: 2
  Dihedral angle restraints: 4057
    sinusoidal: 1620
      harmonic: 2437
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -110.34  179.61     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -65.14  169.74     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" O2G GTP A 501 "
           pdb=" O3B GTP A 501 "
           pdb=" PG  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -45.92 -136.78     1      2.00e+01 2.50e-03 4.15e+01
  ... (remaining 4054 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 540
       0.068 -    0.137: 346
       0.137 -    0.205: 128
       0.205 -    0.274: 22
       0.274 -    0.342: 3
  Chirality restraints: 1039
  Sorted by residual:
  chirality pdb=" CB  ILE D 184 "
            pdb=" CA  ILE D 184 "
            pdb=" CG1 ILE D 184 "
            pdb=" CG2 ILE D 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.93e+00
  chirality pdb=" CB  ILE D  58 "
            pdb=" CA  ILE D  58 "
            pdb=" CG1 ILE D  58 "
            pdb=" CG2 ILE D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CG  LEU D 179 "
            pdb=" CB  LEU D 179 "
            pdb=" CD1 LEU D 179 "
            pdb=" CD2 LEU D 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 1036 not shown)

  Planarity restraints: 1168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  22 "   -0.043 2.00e-02 2.50e+03   2.13e-02 1.14e+01
        pdb=" CG  TRP D  22 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  22 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  22 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  22 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  22 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  22 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  22 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  22 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  22 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D  61 "   -0.016 2.00e-02 2.50e+03   3.36e-02 1.13e+01
        pdb=" C   THR D  61 "    0.058 2.00e-02 2.50e+03
        pdb=" O   THR D  61 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ILE D  62 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 338 "    0.016 2.00e-02 2.50e+03   3.11e-02 9.65e+00
        pdb=" C   TRP A 338 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   TRP A 338 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ILE A 339 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1165 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2119
        2.81 -     3.34: 6518
        3.34 -     3.86: 11061
        3.86 -     4.38: 13731
        4.38 -     4.90: 22092
  Nonbonded interactions: 55521
  Sorted by model distance:
  nonbonded pdb=" N   VAL A 176 "
            pdb=" N   GLU A 177 "
     model   vdw
     2.292 2.560
  nonbonded pdb=" OD1 ASN A 200 "
            pdb=" N2  GTP A 501 "
     model   vdw
     2.384 3.120
  nonbonded pdb=" N   ASP D  95 "
            pdb=" OD1 ASP D  95 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" N   ASP D 174 "
            pdb=" OD1 ASP D 174 "
     model   vdw
     2.434 3.120
  nonbonded pdb=" OD2 ASP D  84 "
            pdb=" NZ  LYS D  86 "
     model   vdw
     2.445 3.120
  ... (remaining 55516 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.040
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6062
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      :  0.023   0.208   6739  Z= 1.207
  Angle     :  1.549  13.804   9123  Z= 0.979
  Chirality :  0.095   0.342   1039
  Planarity :  0.008   0.049   1168
  Dihedral  : 12.465 179.606   2483
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 1.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.30 (0.28), residues: 840
  helix:  0.14 (0.25), residues: 358
  sheet:  1.56 (0.46), residues: 123
  loop : -0.08 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.007   TRP D  22 
 HIS   0.010   0.003   HIS D 321 
 PHE   0.042   0.006   PHE A 313 
 TYR   0.031   0.006   TYR D 394 
 ARG   0.008   0.001   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17422 (  325)
  hydrogen bonds       : angle       6.92545 (  930)
  covalent geometry    : bond        0.02345 ( 6739)
  covalent geometry    : angle       1.54918 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   63 VAL cc_start: 0.7673 (t) cc_final: 0.7265 (p)
REVERT: A  209 LYS cc_start: 0.7361 (mmtt) cc_final: 0.7095 (mtmt)
REVERT: D   36 GLN cc_start: 0.7638 (tp40) cc_final: 0.7351 (mm-40)
REVERT: D   76 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7970 (mtmt)
REVERT: D   81 ASP cc_start: 0.6980 (m-30) cc_final: 0.6530 (t0)
REVERT: D  123 ASP cc_start: 0.7106 (m-30) cc_final: 0.6728 (m-30)
REVERT: D  127 HIS cc_start: 0.6772 (m-70) cc_final: 0.6439 (m170)
REVERT: D  198 MET cc_start: 0.7158 (mtt) cc_final: 0.6705 (ttm)
REVERT: D  249 MET cc_start: 0.6840 (tpp) cc_final: 0.6521 (tpp)
REVERT: D  268 MET cc_start: 0.8358 (mtp) cc_final: 0.7826 (ttp)
REVERT: D  403 GLU cc_start: 0.6689 (tp30) cc_final: 0.6290 (tp30)
REVERT: D  410 ASN cc_start: 0.6799 (m-40) cc_final: 0.6510 (t0)
REVERT: D  417 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6969 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2374
  time to fit residues: 54.9554
Evaluate side-chains
  104 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  12 GLN
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 ASN
D 171 GLN
D 216 ASN
D 279 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.189503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.160235 restraints weight = 6930.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.164418 restraints weight = 4451.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.167114 restraints weight = 3302.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6739  Z= 0.179
  Angle     :  0.658   7.215   9123  Z= 0.359
  Chirality :  0.049   0.183   1039
  Planarity :  0.005   0.054   1168
  Dihedral  : 12.290 165.119    904
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  6.09 %
    Favored  : 91.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.71 (0.29), residues: 840
  helix:  1.06 (0.27), residues: 361
  sheet:  1.24 (0.46), residues: 136
  loop : -0.40 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  22 
 HIS   0.004   0.001   HIS A 260 
 PHE   0.027   0.002   PHE A  97 
 TYR   0.012   0.002   TYR A 306 
 ARG   0.004   0.000   ARG D 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05112 (  325)
  hydrogen bonds       : angle       4.96151 (  930)
  covalent geometry    : bond        0.00411 ( 6739)
  covalent geometry    : angle       0.65804 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A   46 ASP cc_start: 0.7401 (t70) cc_final: 0.7195 (t0)
REVERT: A  222 ASN cc_start: 0.8092 (m-40) cc_final: 0.7252 (m-40)
REVERT: A  367 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7726 (mm-30)
  outliers start: 18
  outliers final: 6
  residues processed: 133
  average time/residue: 0.2020
  time to fit residues: 35.5291
Evaluate side-chains
  93 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0770
   chunk 81 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
D  36 GLN
** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.187623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.158385 restraints weight = 7002.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162428 restraints weight = 4522.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.165003 restraints weight = 3357.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6739  Z= 0.140
  Angle     :  0.555   5.848   9123  Z= 0.300
  Chirality :  0.046   0.165   1039
  Planarity :  0.004   0.049   1168
  Dihedral  : 11.675 160.490    904
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.54 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.81 (0.29), residues: 840
  helix:  1.39 (0.27), residues: 368
  sheet:  0.78 (0.46), residues: 144
  loop : -0.50 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  22 
 HIS   0.003   0.001   HIS A 104 
 PHE   0.016   0.001   PHE A  97 
 TYR   0.008   0.001   TYR A 306 
 ARG   0.004   0.000   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04357 (  325)
  hydrogen bonds       : angle       4.58246 (  930)
  covalent geometry    : bond        0.00327 ( 6739)
  covalent geometry    : angle       0.55466 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8064 (m-40) cc_final: 0.7462 (m-40)
REVERT: D  163 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6958 (ttt)
REVERT: D  192 SER cc_start: 0.7696 (m) cc_final: 0.7493 (p)
REVERT: D  394 TYR cc_start: 0.8931 (m-80) cc_final: 0.8673 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1859
  time to fit residues: 26.3078
Evaluate side-chains
  90 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  418 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 71 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 47 optimal weight:    0.4980
   chunk 29 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
D  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.194153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.164888 restraints weight = 7064.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.168823 restraints weight = 4574.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.171630 restraints weight = 3425.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6739  Z= 0.119
  Angle     :  0.513   6.390   9123  Z= 0.275
  Chirality :  0.045   0.161   1039
  Planarity :  0.004   0.041   1168
  Dihedral  : 11.311 158.451    904
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.51 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.80 (0.29), residues: 840
  helix:  1.46 (0.26), residues: 384
  sheet:  0.85 (0.46), residues: 135
  loop : -0.72 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  22 
 HIS   0.002   0.001   HIS A 104 
 PHE   0.012   0.001   PHE A 313 
 TYR   0.013   0.001   TYR A 191 
 ARG   0.003   0.000   ARG D 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03797 (  325)
  hydrogen bonds       : angle       4.31828 (  930)
  covalent geometry    : bond        0.00272 ( 6739)
  covalent geometry    : angle       0.51292 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.7995 (m-40) cc_final: 0.7419 (m-40)
REVERT: A  239 SER cc_start: 0.9194 (t) cc_final: 0.8975 (p)
REVERT: A  305 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8293 (mtp85)
REVERT: A  416 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6267 (t80)
REVERT: D  163 MET cc_start: 0.7125 (ttt) cc_final: 0.6815 (ttt)
REVERT: D  192 SER cc_start: 0.7825 (m) cc_final: 0.7615 (p)
REVERT: D  206 TYR cc_start: 0.8422 (t80) cc_final: 0.8181 (t80)
REVERT: D  394 TYR cc_start: 0.8879 (m-80) cc_final: 0.8552 (m-80)
  outliers start: 15
  outliers final: 7
  residues processed: 108
  average time/residue: 0.1999
  time to fit residues: 28.6027
Evaluate side-chains
  93 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  416 TYR
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 59 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
D  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.182871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.152722 restraints weight = 7083.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.156632 restraints weight = 4682.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.159124 restraints weight = 3543.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6739  Z= 0.212
  Angle     :  0.598   6.329   9123  Z= 0.320
  Chirality :  0.049   0.159   1039
  Planarity :  0.004   0.047   1168
  Dihedral  : 11.343 159.159    904
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 11.48 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.55 (0.29), residues: 840
  helix:  1.41 (0.26), residues: 377
  sheet:  0.55 (0.45), residues: 135
  loop : -0.94 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 338 
 HIS   0.004   0.001   HIS A 133 
 PHE   0.022   0.002   PHE D 381 
 TYR   0.014   0.002   TYR D  33 
 ARG   0.003   0.001   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04677 (  325)
  hydrogen bonds       : angle       4.43797 (  930)
  covalent geometry    : bond        0.00518 ( 6739)
  covalent geometry    : angle       0.59818 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.7591 (tt) cc_final: 0.7253 (tt)
REVERT: A  123 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7721 (m)
REVERT: A  222 ASN cc_start: 0.8051 (m-40) cc_final: 0.7308 (m-40)
REVERT: A  293 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6572 (mt-10)
REVERT: D  163 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7020 (ttt)
REVERT: D  192 SER cc_start: 0.7860 (m) cc_final: 0.7646 (p)
REVERT: D  304 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7746 (tm-30)
REVERT: D  356 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8160 (mmtp)
REVERT: D  394 TYR cc_start: 0.8991 (m-80) cc_final: 0.8742 (m-80)
  outliers start: 23
  outliers final: 12
  residues processed: 111
  average time/residue: 0.2405
  time to fit residues: 36.6091
Evaluate side-chains
  102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  293 GLU
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  265 MET
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  351 THR
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
D  16 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.188478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.158525 restraints weight = 6974.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.162428 restraints weight = 4606.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.165140 restraints weight = 3488.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.4910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6739  Z= 0.123
  Angle     :  0.522   6.690   9123  Z= 0.277
  Chirality :  0.045   0.160   1039
  Planarity :  0.004   0.040   1168
  Dihedral  : 11.036 154.452    904
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.14 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.61 (0.29), residues: 840
  helix:  1.62 (0.27), residues: 380
  sheet:  0.30 (0.44), residues: 135
  loop : -1.01 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  22 
 HIS   0.002   0.001   HIS A 104 
 PHE   0.023   0.001   PHE A  97 
 TYR   0.014   0.001   TYR A 191 
 ARG   0.003   0.000   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  325)
  hydrogen bonds       : angle       4.29734 (  930)
  covalent geometry    : bond        0.00287 ( 6739)
  covalent geometry    : angle       0.52184 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.7557 (tt) cc_final: 0.7228 (tt)
REVERT: A  123 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7660 (m)
REVERT: A  222 ASN cc_start: 0.7972 (m-40) cc_final: 0.7377 (m-40)
REVERT: A  381 ARG cc_start: 0.7186 (mtm110) cc_final: 0.6983 (ttp-110)
REVERT: D  304 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: D  356 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8166 (mmtp)
REVERT: D  394 TYR cc_start: 0.8890 (m-80) cc_final: 0.8544 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 104
  average time/residue: 0.3034
  time to fit residues: 41.5538
Evaluate side-chains
  99 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  199 ILE
Chi-restraints excluded: chain D residue  214 LYS
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  351 THR
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
D 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.183859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.153191 restraints weight = 7085.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.157072 restraints weight = 4746.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.159538 restraints weight = 3623.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.5026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6739  Z= 0.190
  Angle     :  0.576   6.614   9123  Z= 0.307
  Chirality :  0.048   0.151   1039
  Planarity :  0.004   0.041   1168
  Dihedral  : 11.039 154.598    904
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 13.55 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.41 (0.29), residues: 840
  helix:  1.51 (0.27), residues: 379
  sheet:  0.11 (0.44), residues: 133
  loop : -1.13 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 338 
 HIS   0.003   0.001   HIS A 133 
 PHE   0.019   0.002   PHE D 381 
 TYR   0.012   0.001   TYR D  33 
 ARG   0.002   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04400 (  325)
  hydrogen bonds       : angle       4.31378 (  930)
  covalent geometry    : bond        0.00464 ( 6739)
  covalent geometry    : angle       0.57639 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.7627 (tt) cc_final: 0.7228 (tt)
REVERT: A  123 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7745 (m)
REVERT: A  222 ASN cc_start: 0.8070 (m-40) cc_final: 0.7350 (m-40)
REVERT: D  123 ASP cc_start: 0.6904 (t0) cc_final: 0.6546 (m-30)
REVERT: D  304 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: D  394 TYR cc_start: 0.8954 (m-80) cc_final: 0.8597 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 106
  average time/residue: 0.3058
  time to fit residues: 44.7878
Evaluate side-chains
  103 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 1.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  199 ILE
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  279 HIS
Chi-restraints excluded: chain D residue  351 THR
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.185503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.155110 restraints weight = 7045.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.158991 restraints weight = 4663.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.161563 restraints weight = 3539.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.5127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6739  Z= 0.142
  Angle     :  0.546   6.824   9123  Z= 0.288
  Chirality :  0.046   0.156   1039
  Planarity :  0.004   0.039   1168
  Dihedral  : 10.871 154.492    904
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.66 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.39 (0.29), residues: 840
  helix:  1.60 (0.27), residues: 379
  sheet: -0.04 (0.43), residues: 133
  loop : -1.22 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  22 
 HIS   0.002   0.001   HIS A 104 
 PHE   0.014   0.001   PHE D 381 
 TYR   0.013   0.001   TYR A 191 
 ARG   0.002   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  325)
  hydrogen bonds       : angle       4.25336 (  930)
  covalent geometry    : bond        0.00339 ( 6739)
  covalent geometry    : angle       0.54625 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.7625 (tt) cc_final: 0.7204 (tt)
REVERT: A  123 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7704 (m)
REVERT: A  222 ASN cc_start: 0.7957 (m-40) cc_final: 0.7419 (m-40)
REVERT: A  238 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8255 (m-80)
REVERT: D  123 ASP cc_start: 0.6991 (t0) cc_final: 0.6618 (m-30)
REVERT: D  304 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: D  394 TYR cc_start: 0.8894 (m-80) cc_final: 0.8461 (m-80)
  outliers start: 18
  outliers final: 15
  residues processed: 103
  average time/residue: 0.2056
  time to fit residues: 28.7644
Evaluate side-chains
  104 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  199 ILE
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  279 HIS
Chi-restraints excluded: chain D residue  351 THR
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 57 optimal weight:    0.1980
   chunk 40 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.187872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.157454 restraints weight = 7006.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.161346 restraints weight = 4640.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.164058 restraints weight = 3514.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6739  Z= 0.128
  Angle     :  0.545   9.165   9123  Z= 0.284
  Chirality :  0.046   0.146   1039
  Planarity :  0.004   0.036   1168
  Dihedral  : 10.620 154.170    904
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.80 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.45 (0.29), residues: 840
  helix:  1.68 (0.27), residues: 380
  sheet:  0.00 (0.43), residues: 133
  loop : -1.24 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  22 
 HIS   0.002   0.001   HIS D   9 
 PHE   0.013   0.001   PHE A 313 
 TYR   0.013   0.001   TYR A 191 
 ARG   0.003   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03809 (  325)
  hydrogen bonds       : angle       4.22038 (  930)
  covalent geometry    : bond        0.00303 ( 6739)
  covalent geometry    : angle       0.54508 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.7585 (tt) cc_final: 0.7169 (tt)
REVERT: A  123 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7683 (m)
REVERT: A  222 ASN cc_start: 0.7933 (m-40) cc_final: 0.7388 (m-40)
REVERT: A  238 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8200 (m-80)
REVERT: A  263 MET cc_start: 0.7306 (mtp) cc_final: 0.7081 (mtp)
REVERT: A  381 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7110 (mtm110)
REVERT: D  123 ASP cc_start: 0.7124 (t0) cc_final: 0.6685 (m-30)
REVERT: D  174 ASP cc_start: 0.8161 (p0) cc_final: 0.7881 (p0)
REVERT: D  304 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: D  394 TYR cc_start: 0.8885 (m-80) cc_final: 0.8458 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2833
  time to fit residues: 39.7655
Evaluate side-chains
  105 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  279 HIS
Chi-restraints excluded: chain D residue  351 THR
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    0.0670
   chunk 53 optimal weight:    0.4980
   chunk 29 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0030
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.4928

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.190579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.159681 restraints weight = 7067.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.163648 restraints weight = 4683.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.166406 restraints weight = 3556.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.5378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6739  Z= 0.118
  Angle     :  0.537   9.825   9123  Z= 0.279
  Chirality :  0.045   0.148   1039
  Planarity :  0.003   0.035   1168
  Dihedral  : 10.286 153.929    904
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.77 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.51 (0.29), residues: 840
  helix:  1.73 (0.27), residues: 380
  sheet:  0.12 (0.43), residues: 133
  loop : -1.27 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  22 
 HIS   0.002   0.001   HIS A 104 
 PHE   0.014   0.001   PHE A 313 
 TYR   0.013   0.001   TYR A 191 
 ARG   0.002   0.000   ARG D 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  325)
  hydrogen bonds       : angle       4.18747 (  930)
  covalent geometry    : bond        0.00276 ( 6739)
  covalent geometry    : angle       0.53698 ( 9123)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.7528 (tt) cc_final: 0.7116 (tt)
REVERT: A  123 THR cc_start: 0.7960 (m) cc_final: 0.7633 (m)
REVERT: A  238 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8127 (m-80)
REVERT: A  263 MET cc_start: 0.7280 (mtp) cc_final: 0.7055 (mtp)
REVERT: A  418 LYS cc_start: 0.7935 (pttt) cc_final: 0.7707 (pttp)
REVERT: D  123 ASP cc_start: 0.7107 (t0) cc_final: 0.6646 (m-30)
REVERT: D  174 ASP cc_start: 0.8036 (p0) cc_final: 0.7749 (p0)
REVERT: D  304 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: D  394 TYR cc_start: 0.8882 (m-80) cc_final: 0.8459 (m-80)
REVERT: D  417 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7152 (mt-10)
  outliers start: 13
  outliers final: 12
  residues processed: 103
  average time/residue: 0.2069
  time to fit residues: 28.6400
Evaluate side-chains
  103 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  266 THR
Chi-restraints excluded: chain D residue  279 HIS
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.188347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.157684 restraints weight = 7025.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.161626 restraints weight = 4657.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.164244 restraints weight = 3529.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.5454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6739  Z= 0.133
  Angle     :  0.564  10.368   9123  Z= 0.290
  Chirality :  0.046   0.166   1039
  Planarity :  0.004   0.036   1168
  Dihedral  : 10.118 155.886    904
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.77 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.50 (0.29), residues: 840
  helix:  1.73 (0.27), residues: 380
  sheet:  0.14 (0.43), residues: 133
  loop : -1.29 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  22 
 HIS   0.002   0.001   HIS A 104 
 PHE   0.014   0.001   PHE D 381 
 TYR   0.012   0.001   TYR A 191 
 ARG   0.006   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  325)
  hydrogen bonds       : angle       4.20040 (  930)
  covalent geometry    : bond        0.00318 ( 6739)
  covalent geometry    : angle       0.56362 ( 9123)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2920.02 seconds
wall clock time: 53 minutes 54.89 seconds (3234.89 seconds total)