Starting phenix.real_space_refine
on Thu Feb 13 22:04:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xdg_22137/02_2025/6xdg_22137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xdg_22137/02_2025/6xdg_22137.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xdg_22137/02_2025/6xdg_22137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xdg_22137/02_2025/6xdg_22137.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xdg_22137/02_2025/6xdg_22137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xdg_22137/02_2025/6xdg_22137.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1514 atoms to isotropic.
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      32      5.16       5
     C    5058      2.51       5
     N    1320      2.21       5
     O    1594      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8004
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "E"
      Number of atoms: 1542
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
      Conformer: "B"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
          bond proxies already assigned to first conformer: 1572
    Chain: "D"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1640
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
    Chain: "B"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1603
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1604
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1565
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196}
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  MAN F   4 " occ=0.70
      ... (9 atoms not shown)
      pdb=" O6  MAN F   4 " occ=0.70
  Time building chain proxies: 5.63, per 1000 atoms: 0.70
  Number of scatterers: 8004
  At special positions: 0
  Unit cell: (72.25, 119.85, 150.45, 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      32     16.00
     O    1594      8.00
     N    1320      7.00
     C    5058      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 134 " - pdb=" SG  CYS D 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 147 " - pdb=" SG  CYS B 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 147 " - pdb=" SG  CYS C 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 197 " 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
  Links applied
    ALPHA1-6
      " BMA F   3 " - " MAN F   4 "
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG F   1 " - " ASN E 343 "
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 21 sheets defined
      8.8% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 383 through 389
      removed outlier: 3.753A  pdb=" N   ASP E 389 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 405 through 410
      removed outlier: 4.489A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'D' and resid 121 through 128
    Processing helix  chain 'D' and resid 183 through 189
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 4.257A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.728A  pdb=" N   SER B 195 " --> pdb=" O   PRO B 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.823A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'C' and resid 192 through 196
      removed outlier: 3.975A  pdb=" N   LEU C 196 " --> pdb=" O   SER C 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.798A  pdb=" N   GLN A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 192
      removed outlier: 3.996A  pdb=" N   HIS A 192 " --> pdb=" O   GLN A 188 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.820A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE E 402 " --> pdb=" O   TYR E 508 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP E 436 " --> pdb=" O   ARG E 509 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 453
    Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.758A  pdb=" N   ASP D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 6.431A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   TYR D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LEU D  33 " --> pdb=" O   TYR D  49 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN D  34 " --> pdb=" O   GLN D  89 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN D  89 " --> pdb=" O   ASN D  34 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR D  85 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 118
      removed outlier: 3.513A  pdb=" N   SER D 114 " --> pdb=" O   ASN D 137 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   VAL D 133 " --> pdb=" O   PHE D 118 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   TYR D 173 " --> pdb=" O   ASN D 138 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER D 162 " --> pdb=" O   SER D 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 153 through 155
      removed outlier: 3.730A  pdb=" N   GLN D 155 " --> pdb=" O   TRP D 148 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   TRP D 148 " --> pdb=" O   GLN D 155 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS D 145 " --> pdb=" O   THR D 197 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR D 192 " --> pdb=" O   PHE D 209 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS D 207 " --> pdb=" O   CYS D 194 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.755A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   SER B  25 " --> pdb=" O   GLN B   3 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR B  80 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SER B  71 " --> pdb=" O   TYR B  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 60
      removed outlier: 6.739A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   TYR B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   MET B  34 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP B  99 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94
      removed outlier: 3.658A  pdb=" N   THR B 114 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131
      removed outlier: 3.738A  pdb=" N   SER B 127 " --> pdb=" O   LYS B 150 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA B 143 " --> pdb=" O   VAL B 191 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER B 187 " --> pdb=" O   CYS B 147 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL B 149 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU B 185 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   SER B 184 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   ALA B 175 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   SER B 186 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 161
      removed outlier: 3.717A  pdb=" N   THR B 158 " --> pdb=" O   ASN B 206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.922A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU C  79 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 60
      removed outlier: 3.578A  pdb=" N   TYR C  59 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL C  50 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL C  93 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 131
      removed outlier: 4.472A  pdb=" N   SER C 127 " --> pdb=" O   LYS C 150 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS C 150 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU C 145 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER C 187 " --> pdb=" O   CYS C 147 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TYR C 183 " --> pdb=" O   ASP C 151 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 205 through 206
      removed outlier: 3.515A  pdb=" N   VAL C 205 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C 214 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 9 through 12
      removed outlier: 6.737A  pdb=" N   VAL A  10 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 17 through 23
    Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 51
      removed outlier: 5.444A  pdb=" N   LEU A  48 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN A  40 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASP A  87 " --> pdb=" O   GLN A  40 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER A  92 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 100 " --> pdb=" O   SER A  92 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 118 through 122
      removed outlier: 3.573A  pdb=" N   PHE A 122 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   SER A 141 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA A 178 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER A 169 " --> pdb=" O   ALA A 177 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 118 through 122
      removed outlier: 3.573A  pdb=" N   PHE A 122 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 158 through 159
      removed outlier: 3.565A  pdb=" N   TRP A 152 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN A 198 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    531 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: 2.28

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2535
        1.35 -     1.47: 2165
        1.47 -     1.59: 3460
        1.59 -     1.71: 0
        1.71 -     1.83: 39
  Bond restraints: 8199
  Sorted by residual:
  bond pdb=" C   PHE E 497 "
       pdb=" N   GLN E 498 "
    ideal  model  delta    sigma   weight residual
    1.329  1.293  0.035 1.60e-02 3.91e+03 4.86e+00
  bond pdb=" N   VAL B 176 "
       pdb=" CA  VAL B 176 "
    ideal  model  delta    sigma   weight residual
    1.459  1.441  0.018 1.25e-02 6.40e+03 2.15e+00
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" C5  MAN F   4 "
       pdb=" O5  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.444 -0.026 2.00e-02 2.50e+03 1.65e+00
  bond pdb=" CA  VAL D 110 "
       pdb=" CB  VAL D 110 "
    ideal  model  delta    sigma   weight residual
    1.553  1.544  0.009 7.40e-03 1.83e+04 1.44e+00
  ... (remaining 8194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 10805
        1.62 -     3.24: 296
        3.24 -     4.86: 49
        4.86 -     6.49: 13
        6.49 -     8.11: 8
  Bond angle restraints: 11171
  Sorted by residual:
  angle pdb=" C   PHE E 497 "
        pdb=" N   GLN E 498 "
        pdb=" CA  GLN E 498 "
      ideal   model   delta    sigma   weight residual
     120.49  113.22    7.27 1.42e+00 4.96e-01 2.62e+01
  angle pdb=" C   TYR A  51 "
        pdb=" N   ASP A  52 "
        pdb=" CA  ASP A  52 "
      ideal   model   delta    sigma   weight residual
     121.54  129.53   -7.99 1.91e+00 2.74e-01 1.75e+01
  angle pdb=" C   VAL A  53 "
        pdb=" N   SER A  54 "
        pdb=" CA  SER A  54 "
      ideal   model   delta    sigma   weight residual
     120.23  127.04   -6.81 1.67e+00 3.59e-01 1.66e+01
  angle pdb=" N   SER C 100 "
        pdb=" CA  SER C 100 "
        pdb=" C   SER C 100 "
      ideal   model   delta    sigma   weight residual
     110.33  114.61   -4.28 1.29e+00 6.01e-01 1.10e+01
  angle pdb=" N   ASP A  52 "
        pdb=" CA  ASP A  52 "
        pdb=" C   ASP A  52 "
      ideal   model   delta    sigma   weight residual
     110.80  117.69   -6.89 2.13e+00 2.20e-01 1.05e+01
  ... (remaining 11166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.95: 4633
       21.95 -    43.89: 248
       43.89 -    65.84: 20
       65.84 -    87.78: 13
       87.78 -   109.73: 4
  Dihedral angle restraints: 4918
    sinusoidal: 1898
      harmonic: 3020
  Sorted by residual:
  dihedral pdb=" CA  CYS E 361 "
           pdb=" C   CYS E 361 "
           pdb=" N   VAL E 362 "
           pdb=" CA  VAL E 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.06   25.94     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASP A  52 "
           pdb=" C   ASP A  52 "
           pdb=" N   VAL A  53 "
           pdb=" CA  VAL A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.16   25.84     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  ASP B 108 "
           pdb=" C   ASP B 108 "
           pdb=" N   TYR B 109 "
           pdb=" CA  TYR B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.24  -25.76     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 4915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1150
       0.081 -    0.162: 109
       0.162 -    0.244: 0
       0.244 -    0.325: 2
       0.325 -    0.406: 1
  Chirality restraints: 1262
  Sorted by residual:
  chirality pdb=" C1  MAN F   4 "
            pdb=" O6  BMA F   3 "
            pdb=" C2  MAN F   4 "
            pdb=" O5  MAN F   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.99    0.41 2.00e-02 2.50e+03 4.12e+02
  chirality pdb=" C1  BMA F   3 "
            pdb=" O4  NAG F   2 "
            pdb=" C2  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-02 2.50e+03 1.62e+02
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.76e+01
  ... (remaining 1259 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 155 "    0.028 5.00e-02 4.00e+02   4.22e-02 2.84e+00
        pdb=" N   PRO C 156 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO C 156 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 156 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 110 "   -0.016 2.00e-02 2.50e+03   9.78e-03 2.39e+00
        pdb=" CG  TRP B 110 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 110 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 110 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 110 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 462 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO E 463 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO E 463 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 463 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 317
        2.68 -     3.24: 8293
        3.24 -     3.79: 12628
        3.79 -     4.35: 16251
        4.35 -     4.90: 25992
  Nonbonded interactions: 63481
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 121 "
            pdb=" O   PRO B 130 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" O   PRO C 130 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" O   TYR D 186 "
            pdb=" OH  TYR D 192 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OG  SER D   7 "
            pdb=" OG1 THR D  22 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OD1 ASP A 142 "
            pdb=" NE2 GLN A 171 "
     model   vdw
     2.171 3.120
  ... (remaining 63476 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 
7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 
 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ 
id 79 through 87 or resid 89 through 97 or resid 109 through 220))
  selection = (chain 'C' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 
7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 
 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ 
id 79 through 87 or resid 89 through 97 or resid 109 through 220))
}

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=0.50 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:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.640
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
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      :  0.004   0.035   8199  Z= 0.267
  Angle     :  0.701   8.108  11171  Z= 0.375
  Chirality :  0.046   0.406   1262
  Planarity :  0.004   0.042   1425
  Dihedral  : 13.904 109.730   2968
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 19.43
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.82 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    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: -3.87 (0.23), residues: 1030
  helix: -3.19 (0.52), residues: 48
  sheet: -2.30 (0.24), residues: 377
  loop : -2.77 (0.23), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 110 
 HIS   0.003   0.001   HIS A 201 
 PHE   0.013   0.002   PHE C  68 
 TYR   0.014   0.001   TYR E 495 
 ARG   0.007   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  340 GLU cc_start: 0.9165 (pp20) cc_final: 0.8961 (pp20)
REVERT: E  386 LYS cc_start: 0.9132 (mptt) cc_final: 0.8812 (tptt)
REVERT: E  406 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8660 (mp0)
REVERT: E  432 CYS cc_start: 0.7903 (t) cc_final: 0.7513 (m)
REVERT: E  465 GLU cc_start: 0.7124 (tt0) cc_final: 0.6805 (tt0)
REVERT: E  471 GLU cc_start: 0.8884 (tp30) cc_final: 0.8616 (tm-30)
REVERT: E  515 PHE cc_start: 0.9124 (m-80) cc_final: 0.8896 (m-80)
REVERT: D   93 ASN cc_start: 0.8525 (m110) cc_final: 0.8140 (t0)
REVERT: D  105 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8107 (pt0)
REVERT: D  142 ARG cc_start: 0.8989 (tmt170) cc_final: 0.8500 (ttp80)
REVERT: D  187 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8841 (mm-30)
REVERT: B  199 GLN cc_start: 0.8327 (mt0) cc_final: 0.8068 (tp40)
REVERT: B  216 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8790 (ttpp)
REVERT: C    4 LEU cc_start: 0.8118 (mt) cc_final: 0.7853 (mt)
REVERT: A   49 MET cc_start: 0.8318 (mmm) cc_final: 0.7818 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2824
  time to fit residues: 46.8433
Evaluate side-chains
  87 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 78 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 80 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 93 optimal weight:   30.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
E 388 ASN
E 474 GLN
E 487 ASN
D  38 GLN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  93 ASN
** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 189 HIS
D 210 ASN
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 GLN
B 207 HIS
C   1 GLN
C 162 ASN
C 199 GLN
C 204 ASN
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  81 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.079466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.051607 restraints weight = 70097.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.054791 restraints weight = 24431.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.056777 restraints weight = 13411.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   8199  Z= 0.382
  Angle     :  0.781  11.209  11171  Z= 0.404
  Chirality :  0.047   0.171   1262
  Planarity :  0.005   0.072   1425
  Dihedral  :  8.763  87.660   1210
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 10.11 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.47 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.24), residues: 1030
  helix: -2.52 (0.51), residues: 61
  sheet: -1.65 (0.26), residues: 374
  loop : -2.52 (0.23), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.022   0.002   PHE E 400 
 TYR   0.018   0.002   TYR E 495 
 ARG   0.006   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9149 (mptt) cc_final: 0.8815 (tptt)
REVERT: E  406 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8656 (mp0)
REVERT: E  465 GLU cc_start: 0.7449 (tt0) cc_final: 0.7113 (tt0)
REVERT: E  515 PHE cc_start: 0.9411 (m-80) cc_final: 0.9147 (m-80)
REVERT: D   93 ASN cc_start: 0.8858 (m-40) cc_final: 0.8378 (t0)
REVERT: D  105 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8157 (pt0)
REVERT: D  142 ARG cc_start: 0.8943 (tmt170) cc_final: 0.8534 (ttp80)
REVERT: D  187 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8736 (mm-30)
REVERT: B  199 GLN cc_start: 0.8325 (mt0) cc_final: 0.7993 (tp40)
REVERT: B  216 LYS cc_start: 0.9268 (ttmm) cc_final: 0.8820 (ttpp)
REVERT: C    4 LEU cc_start: 0.8518 (mt) cc_final: 0.8296 (mt)
REVERT: A   38 TYR cc_start: 0.8088 (m-80) cc_final: 0.7740 (m-80)
REVERT: A   49 MET cc_start: 0.8439 (mmm) cc_final: 0.7887 (mmm)
  outliers start: 17
  outliers final: 8
  residues processed: 119
  average time/residue: 0.2805
  time to fit residues: 42.7185
Evaluate side-chains
  93 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain A residue   35 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 33 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0670
   chunk 68 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.1124

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

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 189 HIS
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.082323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.055230 restraints weight = 50087.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.058258 restraints weight = 19878.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.060119 restraints weight = 11446.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8199  Z= 0.192
  Angle     :  0.687   9.370  11171  Z= 0.351
  Chirality :  0.045   0.151   1262
  Planarity :  0.005   0.048   1425
  Dihedral  :  7.831  75.526   1210
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.39 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.48 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.25), residues: 1030
  helix: -2.49 (0.55), residues: 55
  sheet: -1.25 (0.27), residues: 373
  loop : -2.02 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 161 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.012   0.001   PHE E 338 
 TYR   0.011   0.001   TYR E 380 
 ARG   0.004   0.000   ARG E 355 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9089 (mptt) cc_final: 0.8780 (tptt)
REVERT: E  406 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8608 (mp0)
REVERT: E  427 ASP cc_start: 0.9250 (p0) cc_final: 0.9030 (m-30)
REVERT: E  432 CYS cc_start: 0.7363 (m) cc_final: 0.7147 (m)
REVERT: E  465 GLU cc_start: 0.7312 (tt0) cc_final: 0.6945 (tt0)
REVERT: E  515 PHE cc_start: 0.9409 (m-80) cc_final: 0.8555 (m-80)
REVERT: D   93 ASN cc_start: 0.8771 (m-40) cc_final: 0.8294 (t0)
REVERT: D  105 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8150 (pt0)
REVERT: D  142 ARG cc_start: 0.8868 (tmt170) cc_final: 0.8443 (ttp80)
REVERT: B   32 TYR cc_start: 0.8372 (m-80) cc_final: 0.8074 (m-80)
REVERT: B   34 MET cc_start: 0.7970 (mmm) cc_final: 0.7616 (mmm)
REVERT: B  199 GLN cc_start: 0.8405 (mt0) cc_final: 0.8088 (tp40)
REVERT: B  216 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8699 (ttpp)
REVERT: C   87 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8064 (mtm180)
REVERT: A   38 TYR cc_start: 0.8048 (m-80) cc_final: 0.7770 (m-80)
REVERT: A   49 MET cc_start: 0.8433 (mmm) cc_final: 0.7895 (mmm)
  outliers start: 19
  outliers final: 14
  residues processed: 124
  average time/residue: 0.2596
  time to fit residues: 41.5819
Evaluate side-chains
  104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 189 HIS
** C 207 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.080730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.052503 restraints weight = 79101.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.055987 restraints weight = 24565.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.058112 restraints weight = 12842.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8199  Z= 0.285
  Angle     :  0.707  12.160  11171  Z= 0.358
  Chirality :  0.045   0.144   1262
  Planarity :  0.005   0.071   1425
  Dihedral  :  7.245  64.801   1210
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.33 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.05 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    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: -2.41 (0.26), residues: 1030
  helix: -2.24 (0.58), residues: 55
  sheet: -1.02 (0.27), residues: 391
  loop : -1.98 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.028   0.002   PHE C  29 
 TYR   0.027   0.002   TYR E 495 
 ARG   0.011   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9090 (mptt) cc_final: 0.8776 (tptt)
REVERT: E  390 LEU cc_start: 0.6814 (tp) cc_final: 0.6600 (tt)
REVERT: E  406 GLU cc_start: 0.9445 (mt-10) cc_final: 0.8621 (mp0)
REVERT: E  424 LYS cc_start: 0.8953 (tptm) cc_final: 0.8713 (mptm)
REVERT: E  465 GLU cc_start: 0.7343 (tt0) cc_final: 0.7027 (tt0)
REVERT: E  515 PHE cc_start: 0.9331 (m-80) cc_final: 0.8418 (m-80)
REVERT: D    4 MET cc_start: 0.8134 (mmm) cc_final: 0.7851 (mmm)
REVERT: D   93 ASN cc_start: 0.8816 (m-40) cc_final: 0.8351 (t0)
REVERT: D  105 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7796 (mp0)
REVERT: D  142 ARG cc_start: 0.8867 (tmt170) cc_final: 0.8393 (ttp80)
REVERT: B   34 MET cc_start: 0.8131 (mmm) cc_final: 0.7650 (mmm)
REVERT: B   62 ASP cc_start: 0.8595 (t0) cc_final: 0.8341 (t0)
REVERT: B  199 GLN cc_start: 0.8431 (mt0) cc_final: 0.8112 (tp40)
REVERT: B  206 ASN cc_start: 0.7253 (t0) cc_final: 0.6876 (t0)
REVERT: B  216 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8654 (ttpp)
REVERT: C  147 CYS cc_start: 0.7801 (p) cc_final: 0.6548 (m)
REVERT: A   38 TYR cc_start: 0.8134 (m-80) cc_final: 0.7699 (m-80)
REVERT: A   49 MET cc_start: 0.8429 (mmm) cc_final: 0.7916 (mmm)
  outliers start: 22
  outliers final: 17
  residues processed: 117
  average time/residue: 0.2525
  time to fit residues: 38.5285
Evaluate side-chains
  106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 85 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   overall best weight:    3.7586

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

Flipped N/Q/H residues before XYZ refinement:
E 481 ASN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   1 GLN
** C 207 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 = 0.3692 r_free = 0.3692 target = 0.078610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.051774 restraints weight = 48604.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.054570 restraints weight = 19701.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056320 restraints weight = 11422.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8199  Z= 0.350
  Angle     :  0.724  11.201  11171  Z= 0.373
  Chirality :  0.046   0.164   1262
  Planarity :  0.005   0.054   1425
  Dihedral  :  6.861  52.205   1210
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.82 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.28 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    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: -2.38 (0.26), residues: 1030
  helix: -1.96 (0.54), residues: 67
  sheet: -0.96 (0.27), residues: 377
  loop : -1.99 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 110 
 HIS   0.003   0.001   HIS A 201 
 PHE   0.026   0.002   PHE E 497 
 TYR   0.034   0.002   TYR E 495 
 ARG   0.010   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9102 (mptt) cc_final: 0.8772 (tptt)
REVERT: E  406 GLU cc_start: 0.9442 (mt-10) cc_final: 0.8649 (mp0)
REVERT: E  465 GLU cc_start: 0.7427 (tt0) cc_final: 0.6654 (tt0)
REVERT: E  515 PHE cc_start: 0.9363 (m-80) cc_final: 0.8960 (m-80)
REVERT: D   93 ASN cc_start: 0.8880 (m-40) cc_final: 0.8431 (t0)
REVERT: D  105 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7793 (mp0)
REVERT: D  142 ARG cc_start: 0.8898 (tmt170) cc_final: 0.8333 (ttp80)
REVERT: B   62 ASP cc_start: 0.8595 (t0) cc_final: 0.8344 (t0)
REVERT: B  199 GLN cc_start: 0.8409 (mt0) cc_final: 0.8086 (tp40)
REVERT: B  206 ASN cc_start: 0.7406 (t0) cc_final: 0.7042 (t0)
REVERT: B  216 LYS cc_start: 0.9187 (ttmm) cc_final: 0.8678 (ttpp)
REVERT: C  147 CYS cc_start: 0.7855 (p) cc_final: 0.6728 (m)
REVERT: A   38 TYR cc_start: 0.8323 (m-80) cc_final: 0.7712 (m-80)
REVERT: A   49 MET cc_start: 0.8413 (mmm) cc_final: 0.7906 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 116
  average time/residue: 0.2597
  time to fit residues: 39.4109
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   98 ARG
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  165 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 15 optimal weight:    0.4980
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 97 optimal weight:    7.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 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 = 0.3691 r_free = 0.3691 target = 0.078514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.052090 restraints weight = 42424.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.054683 restraints weight = 18352.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.056327 restraints weight = 10959.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8199  Z= 0.329
  Angle     :  0.712   9.538  11171  Z= 0.367
  Chirality :  0.045   0.163   1262
  Planarity :  0.005   0.073   1425
  Dihedral  :  6.476  40.986   1210
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  9.91 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.19 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    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: -2.28 (0.26), residues: 1030
  helix: -1.99 (0.57), residues: 61
  sheet: -1.02 (0.27), residues: 382
  loop : -1.81 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.022   0.002   PHE E 497 
 TYR   0.029   0.002   TYR E 495 
 ARG   0.009   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9089 (mptt) cc_final: 0.8750 (tptt)
REVERT: E  406 GLU cc_start: 0.9459 (mt-10) cc_final: 0.8674 (mp0)
REVERT: E  515 PHE cc_start: 0.9429 (m-80) cc_final: 0.9028 (m-80)
REVERT: D   93 ASN cc_start: 0.8860 (m-40) cc_final: 0.8347 (t0)
REVERT: D  105 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7770 (mp0)
REVERT: D  142 ARG cc_start: 0.8795 (tmt170) cc_final: 0.8298 (ttp80)
REVERT: B   62 ASP cc_start: 0.8570 (t0) cc_final: 0.8327 (t0)
REVERT: B  199 GLN cc_start: 0.8378 (mt0) cc_final: 0.8072 (tp40)
REVERT: B  206 ASN cc_start: 0.7274 (t0) cc_final: 0.6939 (t0)
REVERT: B  216 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8554 (ttpp)
REVERT: C  147 CYS cc_start: 0.7864 (p) cc_final: 0.6779 (m)
REVERT: A   38 TYR cc_start: 0.8260 (m-80) cc_final: 0.7673 (m-80)
REVERT: A   49 MET cc_start: 0.8352 (mmm) cc_final: 0.7851 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 115
  average time/residue: 0.2636
  time to fit residues: 39.3406
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   98 ARG
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  140 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 86 optimal weight:    1.9990
   chunk 76 optimal weight:   50.0000
   chunk 1 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 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 = 0.3796 r_free = 0.3796 target = 0.081886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.054158 restraints weight = 65185.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.057463 restraints weight = 22503.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.059479 restraints weight = 12186.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8199  Z= 0.197
  Angle     :  0.675  10.097  11171  Z= 0.342
  Chirality :  0.045   0.163   1262
  Planarity :  0.005   0.053   1425
  Dihedral  :  5.917  47.025   1210
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.77 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.30 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.27), residues: 1030
  helix: -1.78 (0.60), residues: 61
  sheet: -0.71 (0.29), residues: 367
  loop : -1.63 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.024   0.001   PHE E 497 
 TYR   0.021   0.001   TYR E 495 
 ARG   0.007   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8651 (mp0)
REVERT: E  465 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7317 (tt0)
REVERT: E  468 ILE cc_start: 0.9287 (pt) cc_final: 0.8985 (tp)
REVERT: E  515 PHE cc_start: 0.9394 (m-80) cc_final: 0.9046 (m-80)
REVERT: D    4 MET cc_start: 0.8166 (mmm) cc_final: 0.7939 (mmm)
REVERT: D   93 ASN cc_start: 0.8790 (m-40) cc_final: 0.8344 (t0)
REVERT: D  142 ARG cc_start: 0.8756 (tmt170) cc_final: 0.8243 (ttp80)
REVERT: B   62 ASP cc_start: 0.8583 (t0) cc_final: 0.8341 (t0)
REVERT: B  199 GLN cc_start: 0.8410 (mt0) cc_final: 0.8116 (tp40)
REVERT: B  213 LYS cc_start: 0.9317 (mtpt) cc_final: 0.8846 (tptt)
REVERT: B  216 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8562 (ttpp)
REVERT: C  129 PHE cc_start: 0.8190 (m-10) cc_final: 0.7967 (m-10)
REVERT: C  147 CYS cc_start: 0.7746 (p) cc_final: 0.6571 (m)
REVERT: A   38 TYR cc_start: 0.8027 (m-80) cc_final: 0.7497 (m-80)
REVERT: A   49 MET cc_start: 0.8379 (mmm) cc_final: 0.7811 (mmm)
  outliers start: 25
  outliers final: 19
  residues processed: 119
  average time/residue: 0.2520
  time to fit residues: 39.6417
Evaluate side-chains
  111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue  101 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0070
   chunk 97 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0670
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   overall best weight:    1.0140

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 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 = 0.3815 r_free = 0.3815 target = 0.082678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.055996 restraints weight = 43650.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.058911 restraints weight = 18066.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.060707 restraints weight = 10596.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8199  Z= 0.194
  Angle     :  0.693  10.343  11171  Z= 0.349
  Chirality :  0.045   0.189   1262
  Planarity :  0.005   0.075   1425
  Dihedral  :  5.724  59.740   1210
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.48 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.09 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.27), residues: 1030
  helix: -1.55 (0.63), residues: 61
  sheet: -0.65 (0.28), residues: 373
  loop : -1.46 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 353 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.024   0.002   PHE E 497 
 TYR   0.030   0.001   TYR B  32 
 ARG   0.006   0.000   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8623 (mp0)
REVERT: E  465 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7264 (tt0)
REVERT: E  468 ILE cc_start: 0.9305 (pt) cc_final: 0.9025 (tp)
REVERT: E  515 PHE cc_start: 0.9368 (m-80) cc_final: 0.9059 (m-80)
REVERT: D    4 MET cc_start: 0.8178 (mmm) cc_final: 0.7944 (mmm)
REVERT: D   93 ASN cc_start: 0.8737 (m-40) cc_final: 0.8281 (t0)
REVERT: D  105 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7759 (mp0)
REVERT: D  142 ARG cc_start: 0.8698 (tmt170) cc_final: 0.8183 (ttp80)
REVERT: B   62 ASP cc_start: 0.8575 (t0) cc_final: 0.8309 (t0)
REVERT: B  199 GLN cc_start: 0.8411 (mt0) cc_final: 0.8117 (tp40)
REVERT: C  129 PHE cc_start: 0.8230 (m-10) cc_final: 0.7964 (m-10)
REVERT: C  147 CYS cc_start: 0.7840 (p) cc_final: 0.6774 (m)
REVERT: A   38 TYR cc_start: 0.7919 (m-80) cc_final: 0.7459 (m-80)
REVERT: A   49 MET cc_start: 0.8354 (mmm) cc_final: 0.7804 (mmm)
  outliers start: 26
  outliers final: 21
  residues processed: 120
  average time/residue: 0.2553
  time to fit residues: 39.9558
Evaluate side-chains
  107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  140 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 99 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 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 = 0.3780 r_free = 0.3780 target = 0.080911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.054455 restraints weight = 42952.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.057196 restraints weight = 18174.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.058943 restraints weight = 10775.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8199  Z= 0.260
  Angle     :  0.714  10.118  11171  Z= 0.364
  Chirality :  0.044   0.163   1262
  Planarity :  0.005   0.051   1425
  Dihedral  :  5.726  57.981   1210
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.45 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.65 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.27), residues: 1030
  helix: -1.77 (0.59), residues: 64
  sheet: -0.69 (0.28), residues: 382
  loop : -1.49 (0.27), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C  36 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.033   0.002   PHE E 497 
 TYR   0.025   0.002   TYR A  34 
 ARG   0.005   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  406 GLU cc_start: 0.9430 (mt-10) cc_final: 0.8638 (mp0)
REVERT: E  468 ILE cc_start: 0.9301 (pt) cc_final: 0.9032 (tp)
REVERT: D    4 MET cc_start: 0.8158 (mmm) cc_final: 0.7928 (mmm)
REVERT: D   93 ASN cc_start: 0.8784 (m-40) cc_final: 0.8331 (t0)
REVERT: D  105 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7745 (mp0)
REVERT: D  142 ARG cc_start: 0.8741 (tmt170) cc_final: 0.8211 (ttp80)
REVERT: B   62 ASP cc_start: 0.8569 (t0) cc_final: 0.8297 (t0)
REVERT: B  199 GLN cc_start: 0.8362 (mt0) cc_final: 0.8067 (tp40)
REVERT: B  216 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8575 (ttpp)
REVERT: C  129 PHE cc_start: 0.8165 (m-10) cc_final: 0.7894 (m-10)
REVERT: C  147 CYS cc_start: 0.7776 (p) cc_final: 0.6800 (m)
REVERT: A   38 TYR cc_start: 0.8063 (m-80) cc_final: 0.7502 (m-80)
REVERT: A   49 MET cc_start: 0.8368 (mmm) cc_final: 0.7844 (mmm)
  outliers start: 24
  outliers final: 20
  residues processed: 107
  average time/residue: 0.2240
  time to fit residues: 32.4530
Evaluate side-chains
  104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  140 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 95 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 88 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 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 = 0.3687 r_free = 0.3687 target = 0.078296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.052339 restraints weight = 36086.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.054682 restraints weight = 16987.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.056209 restraints weight = 10588.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3095
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8199  Z= 0.346
  Angle     :  0.753   9.807  11171  Z= 0.386
  Chirality :  0.045   0.179   1262
  Planarity :  0.005   0.077   1425
  Dihedral  :  5.999  59.648   1210
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 17.79
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.50 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.76 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.27), residues: 1030
  helix: -1.79 (0.57), residues: 64
  sheet: -0.86 (0.27), residues: 391
  loop : -1.53 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP C  36 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.034   0.002   PHE E 497 
 TYR   0.035   0.002   TYR A 176 
 ARG   0.004   0.001   ARG B  98 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9087 (mptt) cc_final: 0.8822 (tptt)
REVERT: E  406 GLU cc_start: 0.9446 (mt-10) cc_final: 0.8670 (mp0)
REVERT: E  465 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8002 (tm-30)
REVERT: E  468 ILE cc_start: 0.9325 (pt) cc_final: 0.9054 (tp)
REVERT: D    4 MET cc_start: 0.8156 (mmm) cc_final: 0.7954 (mmm)
REVERT: D   93 ASN cc_start: 0.8890 (m-40) cc_final: 0.8490 (t0)
REVERT: D  105 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7761 (mp0)
REVERT: D  142 ARG cc_start: 0.8745 (tmt170) cc_final: 0.8192 (ttp80)
REVERT: B   62 ASP cc_start: 0.8573 (t0) cc_final: 0.8321 (t0)
REVERT: B  199 GLN cc_start: 0.8379 (mt0) cc_final: 0.8080 (tp40)
REVERT: B  216 LYS cc_start: 0.9162 (ttmm) cc_final: 0.8621 (ttpp)
REVERT: C  129 PHE cc_start: 0.8189 (m-10) cc_final: 0.7913 (m-10)
REVERT: C  147 CYS cc_start: 0.7846 (p) cc_final: 0.7008 (m)
REVERT: A   38 TYR cc_start: 0.8163 (m-80) cc_final: 0.7544 (m-80)
REVERT: A   49 MET cc_start: 0.8368 (mmm) cc_final: 0.7883 (mmm)
  outliers start: 23
  outliers final: 19
  residues processed: 104
  average time/residue: 0.2190
  time to fit residues: 30.9063
Evaluate side-chains
  102 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  510 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  140 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0070
   chunk 43 optimal weight:    0.7980
   chunk 36 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 82 optimal weight:    0.1980
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 204 ASN
** C 207 HIS ** 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 = 0.3799 r_free = 0.3799 target = 0.081874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.054800 restraints weight = 50574.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.057810 restraints weight = 19661.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.059711 restraints weight = 11249.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8199  Z= 0.196
  Angle     :  0.713  10.200  11171  Z= 0.359
  Chirality :  0.045   0.192   1262
  Planarity :  0.005   0.052   1425
  Dihedral  :  5.776  59.021   1210
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.68 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.88 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.07 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.27), residues: 1030
  helix: -1.74 (0.59), residues: 64
  sheet: -0.60 (0.28), residues: 374
  loop : -1.38 (0.27), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C  36 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.027   0.002   PHE E 497 
 TYR   0.035   0.002   TYR A 176 
 ARG   0.006   0.001   ARG E 408 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4383.63 seconds
wall clock time: 78 minutes 56.32 seconds (4736.32 seconds total)