Starting phenix.real_space_refine
on Thu Mar 13 02:49:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vdm_31923/03_2025/7vdm_31923.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vdm_31923/03_2025/7vdm_31923.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2025/7vdm_31923.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2025/7vdm_31923.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2025/7vdm_31923.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vdm_31923/03_2025/7vdm_31923.cif"
  }
  resolution = 2.98
  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=   0.001 sd=   0.008
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      63      5.16       5
     C    5486      2.51       5
     N    1438      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8563
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1744
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2590
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "G"
      Number of atoms: 415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 415
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1749
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 2010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 2010
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 8, 'TRANS': 244}
    Chain: "L"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 27
          Classifications: {'peptide': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 1}
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.87, per 1000 atoms: 0.57
  Number of scatterers: 8563
  At special positions: 0
  Unit cell: (118.56, 108.16, 109.2, 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      63     16.00
     O    1576      8.00
     N    1438      7.00
     C    5486      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.06
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 953.4 milliseconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2038

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      35.3% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 28
      removed outlier: 4.003A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.562A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.567A  pdb=" N   ASP A 229 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 226 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 271 through 279
      removed outlier: 3.784A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 309
      removed outlier: 4.049A  pdb=" N   ALA A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.906A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.595A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 4.366A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 43
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.177A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'R' and resid 33 through 57
    Processing helix  chain 'R' and resid 64 through 95
      removed outlier: 3.733A  pdb=" N   VAL R  68 " --> pdb=" O   PHE R  64 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU R  77 " --> pdb=" O   GLY R  73 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   PHE R  78 " --> pdb=" O   ALA R  74 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ASN R  92 " --> pdb=" O   VAL R  88 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE R  93 " --> pdb=" O   TYR R  89 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE R  94 " --> pdb=" O   LEU R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 133
      removed outlier: 4.056A  pdb=" N   LEU R 120 " --> pdb=" O   GLY R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 140
    Processing helix  chain 'R' and resid 144 through 169
      removed outlier: 3.599A  pdb=" N   VAL R 148 " --> pdb=" O   HIS R 144 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 179 through 212
      removed outlier: 3.864A  pdb=" N   PHE R 183 " --> pdb=" O   TRP R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 235
    Processing helix  chain 'R' and resid 238 through 243
    Processing helix  chain 'R' and resid 245 through 250
      removed outlier: 3.625A  pdb=" N   ILE R 249 " --> pdb=" O   LEU R 245 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 280
      removed outlier: 4.104A  pdb=" N   VAL R 263 " --> pdb=" O   HIS R 259 " (cutoff:3.500A)
      Proline residue:  R 276  - end of helix
      removed outlier: 3.530A  pdb=" N   TYR R 279 " --> pdb=" O   ASN R 275 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.605A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.560A  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: 7.004A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.507A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.652A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.167A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.471A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.624A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.505A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.732A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.732A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 130
      removed outlier: 3.532A  pdb=" N   THR S 201 " --> pdb=" O   SER S 194 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.636A  pdb=" N   TYR S 216 " --> pdb=" O   PHE S 165 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1200 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: 2.30

  Time building geometry restraints manager: 2.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.35: 2712
        1.35 -     1.48: 2341
        1.48 -     1.61: 3611
        1.61 -     1.75: 1
        1.75 -     1.88: 87
  Bond restraints: 8752
  Sorted by residual:
  bond pdb=" C17 CLR R 401 "
       pdb=" C20 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.535  1.668 -0.133 2.00e-02 2.50e+03 4.44e+01
  bond pdb=" C   HIS R 261 "
       pdb=" N   PRO R 262 "
    ideal  model  delta    sigma   weight residual
    1.336  1.393 -0.057 1.20e-02 6.94e+03 2.28e+01
  bond pdb=" CG  LEU B  79 "
       pdb=" CD2 LEU B  79 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.54e+00
  bond pdb=" CG  LEU B 146 "
       pdb=" CD1 LEU B 146 "
    ideal  model  delta    sigma   weight residual
    1.521  1.440  0.081 3.30e-02 9.18e+02 5.96e+00
  bond pdb=" C13 CLR R 401 "
       pdb=" C17 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.598 -0.048 2.00e-02 2.50e+03 5.79e+00
  ... (remaining 8747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.39: 11691
        4.39 -     8.77: 152
        8.77 -    13.16: 19
       13.16 -    17.55: 1
       17.55 -    21.93: 2
  Bond angle restraints: 11865
  Sorted by residual:
  angle pdb=" CA  LEU R 237 "
        pdb=" CB  LEU R 237 "
        pdb=" CG  LEU R 237 "
      ideal   model   delta    sigma   weight residual
     116.30  138.23  -21.93 3.50e+00 8.16e-02 3.93e+01
  angle pdb=" C   ARG L   1 "
        pdb=" N   PRO L   2 "
        pdb=" CA  PRO L   2 "
      ideal   model   delta    sigma   weight residual
     119.84  127.32   -7.48 1.25e+00 6.40e-01 3.58e+01
  angle pdb=" CA  LEU R  45 "
        pdb=" CB  LEU R  45 "
        pdb=" CG  LEU R  45 "
      ideal   model   delta    sigma   weight residual
     116.30  135.77  -19.47 3.50e+00 8.16e-02 3.09e+01
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     121.54  132.11  -10.57 1.91e+00 2.74e-01 3.06e+01
  angle pdb=" N   THR B 143 "
        pdb=" CA  THR B 143 "
        pdb=" C   THR B 143 "
      ideal   model   delta    sigma   weight residual
     112.47  118.75   -6.28 1.24e+00 6.50e-01 2.56e+01
  ... (remaining 11860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4730
       17.86 -    35.72: 390
       35.72 -    53.57: 52
       53.57 -    71.43: 18
       71.43 -    89.29: 5
  Dihedral angle restraints: 5195
    sinusoidal: 2035
      harmonic: 3160
  Sorted by residual:
  dihedral pdb=" CA  LEU R 237 "
           pdb=" C   LEU R 237 "
           pdb=" N   PRO R 238 "
           pdb=" CA  PRO R 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.63   39.37     0      5.00e+00 4.00e-02 6.20e+01
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.18  -69.18     1      1.00e+01 1.00e-02 6.19e+01
  dihedral pdb=" CA  LEU A 268 "
           pdb=" C   LEU A 268 "
           pdb=" N   ASN A 269 "
           pdb=" CA  ASN A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.58  -35.42     0      5.00e+00 4.00e-02 5.02e+01
  ... (remaining 5192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1051
       0.074 -    0.148: 250
       0.148 -    0.222: 37
       0.222 -    0.295: 10
       0.295 -    0.369: 3
  Chirality restraints: 1351
  Sorted by residual:
  chirality pdb=" CG  LEU S 162 "
            pdb=" CB  LEU S 162 "
            pdb=" CD1 LEU S 162 "
            pdb=" CD2 LEU S 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.22   -0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" C14 CLR R 401 "
            pdb=" C13 CLR R 401 "
            pdb=" C15 CLR R 401 "
            pdb=" C8  CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.64    0.32 2.00e-01 2.50e+01 2.53e+00
  chirality pdb=" C9  CLR R 401 "
            pdb=" C10 CLR R 401 "
            pdb=" C11 CLR R 401 "
            pdb=" C8  CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.75    0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 1348 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 237 "    0.064 5.00e-02 4.00e+02   9.73e-02 1.52e+01
        pdb=" N   PRO R 238 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO R 238 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO R 238 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R  32 "   -0.055 5.00e-02 4.00e+02   8.27e-02 1.09e+01
        pdb=" N   PRO R  33 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO R  33 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO R  33 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 275 "    0.046 5.00e-02 4.00e+02   6.87e-02 7.54e+00
        pdb=" N   PRO R 276 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO R 276 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO R 276 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1920
        2.79 -     3.32: 7073
        3.32 -     3.84: 14460
        3.84 -     4.37: 16889
        4.37 -     4.90: 29299
  Nonbonded interactions: 69641
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   THR R 107 "
            pdb=" OG  SER R 161 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG1 THR B 143 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.336 3.040
  ... (remaining 69636 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:             0.600
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.110
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
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   0.133   8752  Z= 0.512
  Angle     :  1.291  21.931  11865  Z= 0.678
  Chirality :  0.066   0.369   1351
  Planarity :  0.008   0.097   1486
  Dihedral  : 13.650  89.286   3148
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.75 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.19 %

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: -2.74 (0.22), residues: 1078
  helix: -2.29 (0.20), residues: 363
  sheet: -0.82 (0.29), residues: 299
  loop : -1.91 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B  63 
 HIS   0.010   0.003   HIS B 142 
 PHE   0.028   0.003   PHE B 199 
 TYR   0.024   0.004   TYR R 222 
 ARG   0.025   0.001   ARG B 134 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7023 (mtm-85) cc_final: 0.6685 (ptp-110)
REVERT: A   26 ASP cc_start: 0.7134 (m-30) cc_final: 0.6880 (m-30)
  outliers start: 2
  outliers final: 2
  residues processed: 143
  average time/residue: 1.4547
  time to fit residues: 220.6992
Evaluate side-chains
  103 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain L residue    1 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0980
   chunk 42 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN
B 340 ASN
G  18 GLN
S 182 ASN
R  48 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.178914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.142533 restraints weight = 9283.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 1.72
r_work: 0.3369 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8752  Z= 0.224
  Angle     :  0.648  12.500  11865  Z= 0.332
  Chirality :  0.043   0.159   1351
  Planarity :  0.005   0.073   1486
  Dihedral  :  6.471  69.432   1250
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.08 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.17 (0.24), residues: 1078
  helix:  0.09 (0.26), residues: 368
  sheet: -0.68 (0.29), residues: 294
  loop : -1.53 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.014   0.001   PHE A 223 
 TYR   0.029   0.002   TYR R 222 
 ARG   0.007   0.000   ARG B  19 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.6873 (ptp-110)
REVERT: A  306 GLN cc_start: 0.6939 (mm110) cc_final: 0.6508 (mm110)
REVERT: B   19 ARG cc_start: 0.7406 (ttp80) cc_final: 0.7079 (ttp-170)
REVERT: B  323 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7397 (m-30)
REVERT: S  128 MET cc_start: 0.7083 (mmp) cc_final: 0.6868 (mmm)
REVERT: R  222 TYR cc_start: 0.6368 (p90) cc_final: 0.5953 (p90)
  outliers start: 20
  outliers final: 9
  residues processed: 120
  average time/residue: 1.4241
  time to fit residues: 180.9693
Evaluate side-chains
  110 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0870
   chunk 87 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0270
   chunk 59 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    2.6222

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 331 ASN
B 175 GLN
B 340 ASN
S 159 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.175201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.138572 restraints weight = 9365.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 1.95
r_work: 0.3279 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090   8752  Z= 0.356
  Angle     :  0.701  13.167  11865  Z= 0.359
  Chirality :  0.045   0.152   1351
  Planarity :  0.005   0.067   1486
  Dihedral  :  6.162  68.341   1243
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.37 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.77 (0.25), residues: 1078
  helix:  0.79 (0.27), residues: 366
  sheet: -0.71 (0.29), residues: 290
  loop : -1.45 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP S  36 
 HIS   0.007   0.002   HIS B  91 
 PHE   0.018   0.002   PHE A 223 
 TYR   0.026   0.002   TYR R 222 
 ARG   0.007   0.001   ARG S 168 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 113
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A  251 ASP cc_start: 0.8066 (t0) cc_final: 0.7791 (t0)
REVERT: A  306 GLN cc_start: 0.6834 (mm110) cc_final: 0.6404 (mm110)
REVERT: A  349 LYS cc_start: 0.8494 (ttmp) cc_final: 0.8054 (ttpm)
REVERT: B   19 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7251 (ttp-170)
REVERT: G   38 MET cc_start: 0.7984 (ttp) cc_final: 0.7714 (ttp)
REVERT: G   58 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7863 (pm20)
REVERT: R   61 ARG cc_start: 0.7347 (ptp90) cc_final: 0.6821 (ptp-110)
REVERT: R  222 TYR cc_start: 0.6367 (p90) cc_final: 0.5911 (p90)
  outliers start: 35
  outliers final: 16
  residues processed: 135
  average time/residue: 1.2511
  time to fit residues: 179.6917
Evaluate side-chains
  120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0050
   chunk 47 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.1600

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 331 ASN
B 142 HIS
B 175 GLN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.179044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.142988 restraints weight = 9321.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.80
r_work: 0.3342 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8752  Z= 0.202
  Angle     :  0.589  10.114  11865  Z= 0.301
  Chirality :  0.042   0.153   1351
  Planarity :  0.004   0.059   1486
  Dihedral  :  5.643  70.712   1243
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.34 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.26 (0.26), residues: 1078
  helix:  1.36 (0.27), residues: 362
  sheet: -0.53 (0.30), residues: 286
  loop : -1.19 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.015   0.002   HIS B 142 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.021   0.002   TYR R 222 
 ARG   0.008   0.000   ARG S 168 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.6982 (ptp-110)
REVERT: A  306 GLN cc_start: 0.6876 (mm110) cc_final: 0.6442 (mm110)
REVERT: A  349 LYS cc_start: 0.8464 (ttmp) cc_final: 0.8018 (ttpm)
REVERT: B  323 ASP cc_start: 0.7799 (m-30) cc_final: 0.7322 (m-30)
REVERT: G   37 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (mp)
REVERT: G   38 MET cc_start: 0.7914 (ttp) cc_final: 0.7635 (ttp)
REVERT: S   76 LYS cc_start: 0.7560 (tptp) cc_final: 0.7311 (tptp)
REVERT: R   61 ARG cc_start: 0.7284 (ptp90) cc_final: 0.6846 (ptp-110)
REVERT: R  222 TYR cc_start: 0.6420 (p90) cc_final: 0.5842 (p90)
  outliers start: 29
  outliers final: 15
  residues processed: 136
  average time/residue: 1.2432
  time to fit residues: 179.8574
Evaluate side-chains
  121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 5 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 333 GLN
B 175 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.178792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.142755 restraints weight = 9293.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 1.84
r_work: 0.3358 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8752  Z= 0.186
  Angle     :  0.570   9.675  11865  Z= 0.292
  Chirality :  0.041   0.159   1351
  Planarity :  0.004   0.056   1486
  Dihedral  :  5.418  71.914   1243
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.85 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.03 (0.26), residues: 1078
  helix:  1.69 (0.28), residues: 362
  sheet: -0.47 (0.30), residues: 289
  loop : -1.04 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.018   0.001   TYR R 222 
 ARG   0.008   0.000   ARG B  19 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A  306 GLN cc_start: 0.6897 (mm110) cc_final: 0.6451 (mm110)
REVERT: A  349 LYS cc_start: 0.8394 (ttmp) cc_final: 0.7968 (ttpm)
REVERT: B   19 ARG cc_start: 0.7303 (ttp80) cc_final: 0.7047 (ttp-170)
REVERT: B  219 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7662 (mmm160)
REVERT: B  323 ASP cc_start: 0.7637 (m-30) cc_final: 0.7144 (m-30)
REVERT: G   38 MET cc_start: 0.7857 (ttp) cc_final: 0.7566 (ttp)
REVERT: S   76 LYS cc_start: 0.7537 (tptp) cc_final: 0.7299 (tptp)
REVERT: R   61 ARG cc_start: 0.7170 (ptp90) cc_final: 0.6768 (ptp-110)
  outliers start: 32
  outliers final: 15
  residues processed: 132
  average time/residue: 1.1936
  time to fit residues: 168.2722
Evaluate side-chains
  119 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  194 LEU
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 331 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 159 ASN ** 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 = 0.4035 r_free = 0.4035 target = 0.181362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.145251 restraints weight = 9143.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.81
r_work: 0.3348 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8752  Z= 0.218
  Angle     :  0.595  11.466  11865  Z= 0.302
  Chirality :  0.042   0.157   1351
  Planarity :  0.004   0.053   1486
  Dihedral  :  5.450  71.582   1243
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.85 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.15 (0.26), residues: 1078
  helix:  1.78 (0.28), residues: 363
  sheet: -0.33 (0.30), residues: 285
  loop : -1.02 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.011   0.001   PHE R 104 
 TYR   0.016   0.002   TYR R 222 
 ARG   0.007   0.000   ARG B  19 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.6792 (ptp-110)
REVERT: A  306 GLN cc_start: 0.6895 (mm110) cc_final: 0.6360 (mm110)
REVERT: A  349 LYS cc_start: 0.8407 (ttmp) cc_final: 0.7976 (ttpm)
REVERT: B   19 ARG cc_start: 0.7308 (ttp80) cc_final: 0.6983 (ttp-170)
REVERT: B  219 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7645 (mmm160)
REVERT: B  234 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8396 (m-80)
REVERT: B  323 ASP cc_start: 0.7702 (m-30) cc_final: 0.7187 (m-30)
REVERT: G   38 MET cc_start: 0.7853 (ttp) cc_final: 0.7562 (ttp)
REVERT: S   76 LYS cc_start: 0.7553 (tptp) cc_final: 0.7323 (tptp)
REVERT: R   61 ARG cc_start: 0.7189 (ptp90) cc_final: 0.6727 (ptp-110)
  outliers start: 29
  outliers final: 15
  residues processed: 134
  average time/residue: 1.3059
  time to fit residues: 185.8033
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  194 LEU
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    0.0970
   chunk 102 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 84 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 331 ASN
A 333 GLN
B  88 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.182243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.147672 restraints weight = 9203.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.84
r_work: 0.3354 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8752  Z= 0.161
  Angle     :  0.569  13.552  11865  Z= 0.284
  Chirality :  0.041   0.163   1351
  Planarity :  0.004   0.052   1486
  Dihedral  :  5.225  72.924   1243
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.92 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 (0.26), residues: 1078
  helix:  1.98 (0.28), residues: 363
  sheet: -0.36 (0.30), residues: 289
  loop : -0.92 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.011   0.001   PHE R 104 
 TYR   0.013   0.001   TYR R 222 
 ARG   0.009   0.000   ARG S 168 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.980 
Fit side-chains
REVERT: A  243 MET cc_start: 0.7470 (mmt) cc_final: 0.7182 (tpp)
REVERT: A  306 GLN cc_start: 0.6862 (mm110) cc_final: 0.6404 (mm110)
REVERT: A  349 LYS cc_start: 0.8437 (ttmp) cc_final: 0.7999 (ttpm)
REVERT: B   19 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7098 (ttp-170)
REVERT: B  219 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7622 (mmm160)
REVERT: B  234 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8390 (m-80)
REVERT: B  269 ILE cc_start: 0.7260 (mp) cc_final: 0.6955 (mt)
REVERT: G   38 MET cc_start: 0.7838 (ttp) cc_final: 0.7549 (ttp)
REVERT: R   61 ARG cc_start: 0.7081 (ptp90) cc_final: 0.6713 (ptp-110)
  outliers start: 26
  outliers final: 12
  residues processed: 138
  average time/residue: 1.2596
  time to fit residues: 184.8296
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 85 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 331 ASN
A 333 GLN
** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.177423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.141192 restraints weight = 9302.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.01
r_work: 0.3259 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.091   8752  Z= 0.361
  Angle     :  0.701  14.417  11865  Z= 0.353
  Chirality :  0.046   0.153   1351
  Planarity :  0.004   0.053   1486
  Dihedral  :  5.811  69.682   1243
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 17.96 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.00 (0.26), residues: 1078
  helix:  1.64 (0.27), residues: 366
  sheet: -0.38 (0.29), residues: 295
  loop : -1.15 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP S  36 
 HIS   0.006   0.002   HIS B  91 
 PHE   0.016   0.002   PHE A 196 
 TYR   0.021   0.002   TYR S  94 
 ARG   0.009   0.001   ARG S 168 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A  243 MET cc_start: 0.7469 (mmt) cc_final: 0.7086 (tpp)
REVERT: A  306 GLN cc_start: 0.6901 (mm110) cc_final: 0.6399 (mm110)
REVERT: A  349 LYS cc_start: 0.8507 (ttmp) cc_final: 0.8034 (ttpm)
REVERT: B   19 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7198 (ttp-170)
REVERT: B   38 ASP cc_start: 0.7650 (m-30) cc_final: 0.7399 (m-30)
REVERT: B  219 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7582 (mmm160)
REVERT: B  234 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8370 (m-80)
REVERT: B  323 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7498 (m-30)
REVERT: R   52 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6634 (mt)
REVERT: R   61 ARG cc_start: 0.7288 (ptp90) cc_final: 0.6788 (ptp-110)
  outliers start: 39
  outliers final: 19
  residues processed: 145
  average time/residue: 1.2748
  time to fit residues: 196.2094
Evaluate side-chains
  134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  194 LEU
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  233 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 101 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0010
   chunk 92 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
** S 159 ASN ** 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 = 0.4017 r_free = 0.4017 target = 0.179862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.142816 restraints weight = 9234.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.97
r_work: 0.3338 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8752  Z= 0.173
  Angle     :  0.593  13.806  11865  Z= 0.294
  Chirality :  0.042   0.163   1351
  Planarity :  0.004   0.049   1486
  Dihedral  :  5.293  72.007   1243
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 20.11 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.31 (0.26), residues: 1078
  helix:  1.94 (0.28), residues: 363
  sheet: -0.27 (0.30), residues: 286
  loop : -0.94 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.012   0.001   TYR R 222 
 ARG   0.006   0.000   ARG B  19 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.982 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.6893 (ptp-110)
REVERT: A  243 MET cc_start: 0.7406 (mmt) cc_final: 0.7177 (tpp)
REVERT: A  306 GLN cc_start: 0.6857 (mm110) cc_final: 0.6329 (mm110)
REVERT: A  349 LYS cc_start: 0.8420 (ttmp) cc_final: 0.7975 (ttpm)
REVERT: B   19 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7148 (ttp-170)
REVERT: B   38 ASP cc_start: 0.7511 (m-30) cc_final: 0.7238 (m-30)
REVERT: B  219 ARG cc_start: 0.8229 (mmm160) cc_final: 0.7607 (mmm160)
REVERT: B  234 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8367 (m-80)
REVERT: B  323 ASP cc_start: 0.7670 (m-30) cc_final: 0.7166 (m-30)
REVERT: S   83 MET cc_start: 0.6662 (mmt) cc_final: 0.6459 (mpp)
REVERT: R   61 ARG cc_start: 0.7084 (ptp90) cc_final: 0.6653 (ptp-110)
  outliers start: 19
  outliers final: 11
  residues processed: 135
  average time/residue: 1.2179
  time to fit residues: 175.1112
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 64 optimal weight:    0.1980
   chunk 76 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 99 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   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 204 GLN
A 269 ASN
A 331 ASN
B 142 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.181318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.145200 restraints weight = 9202.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.90
r_work: 0.3349 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8752  Z= 0.160
  Angle     :  0.595  14.262  11865  Z= 0.293
  Chirality :  0.042   0.166   1351
  Planarity :  0.004   0.047   1486
  Dihedral  :  5.157  73.442   1243
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.08 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.44 (0.26), residues: 1078
  helix:  2.19 (0.28), residues: 361
  sheet: -0.32 (0.30), residues: 294
  loop : -0.89 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.011   0.001   HIS B 142 
 PHE   0.013   0.001   PHE R  81 
 TYR   0.011   0.001   TYR R 222 
 ARG   0.006   0.000   ARG S 168 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A  204 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6663 (tp-100)
REVERT: A  245 GLU cc_start: 0.6446 (tp30) cc_final: 0.6146 (mp0)
REVERT: A  306 GLN cc_start: 0.6858 (mm110) cc_final: 0.6404 (mm110)
REVERT: A  349 LYS cc_start: 0.8424 (ttmp) cc_final: 0.7975 (ttpm)
REVERT: B   19 ARG cc_start: 0.7327 (ttp80) cc_final: 0.7064 (ttp-170)
REVERT: B  219 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7591 (mmm160)
REVERT: B  234 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8407 (m-80)
REVERT: G   38 MET cc_start: 0.7812 (ttp) cc_final: 0.7527 (ttp)
REVERT: R   61 ARG cc_start: 0.7036 (ptp90) cc_final: 0.6604 (ptp-110)
  outliers start: 15
  outliers final: 10
  residues processed: 129
  average time/residue: 1.3041
  time to fit residues: 178.6358
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 23 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    0.3980
   chunk 87 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0070
   chunk 78 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.8202

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** 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 = 0.4027 r_free = 0.4027 target = 0.180961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.144415 restraints weight = 9256.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.93
r_work: 0.3346 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.133   8752  Z= 0.269
  Angle     :  0.945  59.199  11865  Z= 0.528
  Chirality :  0.050   0.959   1351
  Planarity :  0.004   0.047   1486
  Dihedral  :  5.174  73.437   1243
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.72 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.43 (0.26), residues: 1078
  helix:  2.19 (0.28), residues: 361
  sheet: -0.29 (0.30), residues: 289
  loop : -0.94 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.009   0.001   HIS B 142 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R 222 
 ARG   0.005   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7166.10 seconds
wall clock time: 124 minutes 46.78 seconds (7486.78 seconds total)