Starting phenix.real_space_refine
on Sun Jul 27 14:20:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xdg_22137/07_2025/6xdg_22137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xdg_22137/07_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_22137/07_2025/6xdg_22137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xdg_22137/07_2025/6xdg_22137.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xdg_22137/07_2025/6xdg_22137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xdg_22137/07_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.66, per 1000 atoms: 0.71
  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: 2.09
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.01
  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: 2.42

  Time building geometry restraints manager: 2.45 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:             6.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.960
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.070
-------------------------------------------------------------------------------
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   0.065   8213  Z= 0.210
  Angle     :  0.897  46.634  11203  Z= 0.419
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       2.27813 (    3)
  link_ALPHA1-6        : bond        0.06424 (    1)
  link_ALPHA1-6        : angle      12.26008 (    3)
  link_BETA1-4         : bond        0.06496 (    2)
  link_BETA1-4         : angle      22.48496 (    6)
  hydrogen bonds       : bond        0.33702 (  205)
  hydrogen bonds       : angle      11.45147 (  531)
  SS BOND              : bond        0.00292 (   10)
  SS BOND              : angle       1.07632 (   20)
  covalent geometry    : bond        0.00406 ( 8199)
  covalent geometry    : angle       0.70083 (11171)

*********************** 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  : 0.869 
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: 0.2891
  time to fit residues: 48.1212
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  : 0.908 
-------------------------------------------------------------------------------
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 = 58)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.051615 restraints weight = 70097.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.054800 restraints weight = 24423.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.056788 restraints weight = 13400.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    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 = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
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   8213  Z= 0.273
  Angle     :  0.791  11.209  11203  Z= 0.407
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       1.53294 (    3)
  link_ALPHA1-6        : bond        0.02142 (    1)
  link_ALPHA1-6        : angle       1.94621 (    3)
  link_BETA1-4         : bond        0.01016 (    2)
  link_BETA1-4         : angle       4.23376 (    6)
  hydrogen bonds       : bond        0.05596 (  205)
  hydrogen bonds       : angle       8.39975 (  531)
  SS BOND              : bond        0.00433 (   10)
  SS BOND              : angle       1.78745 (   20)
  covalent geometry    : bond        0.00586 ( 8199)
  covalent geometry    : angle       0.78137 (11171)

*********************** 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  : 0.959 
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: 0.7450 (tt0) cc_final: 0.7114 (tt0)
REVERT: E  515 PHE cc_start: 0.9412 (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: 0.9269 (ttmm) cc_final: 0.8820 (ttpp)
REVERT: C    4 LEU cc_start: 0.8518 (mt) cc_final: 0.8297 (mt)
REVERT: A   38 TYR cc_start: 0.8087 (m-80) cc_final: 0.7740 (m-80)
REVERT: A   49 MET cc_start: 0.8438 (mmm) cc_final: 0.7886 (mmm)
  outliers start: 17
  outliers final: 8
  residues processed: 119
  average time/residue: 0.2666
  time to fit residues: 40.7534
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  : 0.868 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0470
   chunk 68 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.1482

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.082293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.055222 restraints weight = 49830.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.058231 restraints weight = 19491.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.060065 restraints weight = 11176.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8213  Z= 0.131
  Angle     :  0.697   9.375  11203  Z= 0.353
  Chirality :  0.045   0.152   1262
  Planarity :  0.004   0.047   1425
  Dihedral  :  7.832  75.467   1210
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.48 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.59 %
    Favored  : 83.16 %
  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: -2.62 (0.25), residues: 1030
  helix: -2.49 (0.55), residues: 55
  sheet: -1.22 (0.27), residues: 366
  loop : -2.04 (0.24), residues: 609

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 365 
 ARG   0.003   0.000   ARG E 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00156 (    1)
  link_NAG-ASN         : angle       0.86665 (    3)
  link_ALPHA1-6        : bond        0.01237 (    1)
  link_ALPHA1-6        : angle       2.29367 (    3)
  link_BETA1-4         : bond        0.00744 (    2)
  link_BETA1-4         : angle       3.87372 (    6)
  hydrogen bonds       : bond        0.04130 (  205)
  hydrogen bonds       : angle       7.76173 (  531)
  SS BOND              : bond        0.00352 (   10)
  SS BOND              : angle       1.60532 (   20)
  covalent geometry    : bond        0.00289 ( 8199)
  covalent geometry    : angle       0.68785 (11171)

*********************** 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
  127 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.849 
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: 0.9094 (mptt) cc_final: 0.8785 (tptt)
REVERT: E  406 GLU cc_start: 0.9380 (mt-10) cc_final: 0.8630 (mp0)
REVERT: E  427 ASP cc_start: 0.9240 (p0) cc_final: 0.9024 (m-30)
REVERT: E  465 GLU cc_start: 0.7323 (tt0) cc_final: 0.6958 (tt0)
REVERT: E  515 PHE cc_start: 0.9391 (m-80) cc_final: 0.8532 (m-80)
REVERT: D   93 ASN cc_start: 0.8781 (m-40) cc_final: 0.8308 (t0)
REVERT: D  105 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8154 (pt0)
REVERT: D  142 ARG cc_start: 0.8865 (tmt170) cc_final: 0.8446 (ttp80)
REVERT: B   34 MET cc_start: 0.7955 (mmm) cc_final: 0.7527 (mmm)
REVERT: B  199 GLN cc_start: 0.8408 (mt0) cc_final: 0.8091 (tp40)
REVERT: B  216 LYS cc_start: 0.9169 (ttmm) cc_final: 0.8711 (ttpp)
REVERT: C   87 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8063 (mtm180)
REVERT: A   38 TYR cc_start: 0.8069 (m-80) cc_final: 0.7766 (m-80)
REVERT: A   49 MET cc_start: 0.8442 (mmm) cc_final: 0.7901 (mmm)
  outliers start: 19
  outliers final: 14
  residues processed: 123
  average time/residue: 0.2529
  time to fit residues: 40.1159
Evaluate side-chains
  105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 51 optimal weight:    0.0470
   chunk 48 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    2.2086

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.081390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.053036 restraints weight = 79016.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.056586 restraints weight = 24787.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.058736 restraints weight = 13030.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8213  Z= 0.172
  Angle     :  0.708  11.972  11203  Z= 0.355
  Chirality :  0.045   0.144   1262
  Planarity :  0.005   0.071   1425
  Dihedral  :  7.203  65.100   1210
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.65 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.94 %
    Favored  : 81.48 %
  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: -2.36 (0.26), residues: 1030
  helix: -2.24 (0.58), residues: 55
  sheet: -0.93 (0.27), residues: 376
  loop : -1.96 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 161 
 HIS   0.003   0.001   HIS A 201 
 PHE   0.024   0.002   PHE C  29 
 TYR   0.024   0.002   TYR E 495 
 ARG   0.002   0.000   ARG D 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00060 (    1)
  link_NAG-ASN         : angle       1.00773 (    3)
  link_ALPHA1-6        : bond        0.01063 (    1)
  link_ALPHA1-6        : angle       2.00115 (    3)
  link_BETA1-4         : bond        0.00589 (    2)
  link_BETA1-4         : angle       3.70141 (    6)
  hydrogen bonds       : bond        0.03697 (  205)
  hydrogen bonds       : angle       7.35259 (  531)
  SS BOND              : bond        0.00416 (   10)
  SS BOND              : angle       1.80733 (   20)
  covalent geometry    : bond        0.00376 ( 8199)
  covalent geometry    : angle       0.69892 (11171)

*********************** 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
  124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.846 
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  386 LYS cc_start: 0.9085 (mptt) cc_final: 0.8749 (tptt)
REVERT: E  406 GLU cc_start: 0.9469 (mt-10) cc_final: 0.8641 (mp0)
REVERT: E  424 LYS cc_start: 0.8970 (tptm) cc_final: 0.8715 (mptm)
REVERT: E  465 GLU cc_start: 0.7301 (tt0) cc_final: 0.6989 (tt0)
REVERT: E  515 PHE cc_start: 0.9317 (m-80) cc_final: 0.8933 (m-80)
REVERT: D    4 MET cc_start: 0.8177 (mmm) cc_final: 0.7870 (mmm)
REVERT: D   93 ASN cc_start: 0.8785 (m-40) cc_final: 0.8318 (t0)
REVERT: D  105 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7773 (mp0)
REVERT: D  142 ARG cc_start: 0.8884 (tmt170) cc_final: 0.8425 (ttp80)
REVERT: B   32 TYR cc_start: 0.8368 (m-80) cc_final: 0.8062 (m-80)
REVERT: B   34 MET cc_start: 0.8033 (mmm) cc_final: 0.7583 (mmm)
REVERT: B   62 ASP cc_start: 0.8602 (t0) cc_final: 0.8336 (t0)
REVERT: B  199 GLN cc_start: 0.8408 (mt0) cc_final: 0.8088 (tp40)
REVERT: B  206 ASN cc_start: 0.7229 (t0) cc_final: 0.6857 (t0)
REVERT: B  216 LYS cc_start: 0.9169 (ttmm) cc_final: 0.8641 (ttpp)
REVERT: C  147 CYS cc_start: 0.7751 (p) cc_final: 0.6473 (m)
REVERT: A   38 TYR cc_start: 0.8091 (m-80) cc_final: 0.7731 (m-80)
REVERT: A   49 MET cc_start: 0.8438 (mmm) cc_final: 0.7915 (mmm)
  outliers start: 22
  outliers final: 16
  residues processed: 121
  average time/residue: 0.2578
  time to fit residues: 40.3122
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 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:    7.9990
   chunk 85 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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**
D 189 HIS
B   1 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.077848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.051009 restraints weight = 47339.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.053693 restraints weight = 19580.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.055397 restraints weight = 11545.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8213  Z= 0.289
  Angle     :  0.752   9.247  11203  Z= 0.388
  Chirality :  0.046   0.164   1262
  Planarity :  0.005   0.049   1425
  Dihedral  :  6.883  50.393   1210
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 20.51
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.01 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.40 %
    Favored  : 79.24 %
  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: -2.48 (0.26), residues: 1030
  helix: -2.03 (0.53), residues: 67
  sheet: -1.00 (0.27), residues: 384
  loop : -2.09 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 110 
 HIS   0.003   0.001   HIS A 201 
 PHE   0.050   0.003   PHE E 497 
 TYR   0.039   0.002   TYR E 495 
 ARG   0.004   0.001   ARG B  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00229 (    1)
  link_NAG-ASN         : angle       1.67227 (    3)
  link_ALPHA1-6        : bond        0.01023 (    1)
  link_ALPHA1-6        : angle       1.84638 (    3)
  link_BETA1-4         : bond        0.00574 (    2)
  link_BETA1-4         : angle       3.60525 (    6)
  hydrogen bonds       : bond        0.04209 (  205)
  hydrogen bonds       : angle       7.34459 (  531)
  SS BOND              : bond        0.00399 (   10)
  SS BOND              : angle       2.13034 (   20)
  covalent geometry    : bond        0.00617 ( 8199)
  covalent geometry    : angle       0.74200 (11171)

*********************** 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
  120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 1.089 
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: 0.9108 (mptt) cc_final: 0.8777 (tptt)
REVERT: E  406 GLU cc_start: 0.9455 (mt-10) cc_final: 0.8693 (mp0)
REVERT: E  465 GLU cc_start: 0.7454 (tt0) cc_final: 0.6668 (tt0)
REVERT: E  515 PHE cc_start: 0.9386 (m-80) cc_final: 0.8972 (m-80)
REVERT: D   93 ASN cc_start: 0.8899 (m-40) cc_final: 0.8385 (t0)
REVERT: D  105 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7799 (mp0)
REVERT: D  142 ARG cc_start: 0.8876 (tmt170) cc_final: 0.8323 (ttp80)
REVERT: B   62 ASP cc_start: 0.8554 (t0) cc_final: 0.8300 (t0)
REVERT: B  199 GLN cc_start: 0.8385 (mt0) cc_final: 0.8067 (tp40)
REVERT: B  206 ASN cc_start: 0.7441 (t0) cc_final: 0.7074 (t0)
REVERT: B  216 LYS cc_start: 0.9188 (ttmm) cc_final: 0.8671 (ttpp)
REVERT: C  147 CYS cc_start: 0.7998 (p) cc_final: 0.6915 (m)
REVERT: A   38 TYR cc_start: 0.8343 (m-80) cc_final: 0.7700 (m-80)
REVERT: A   49 MET cc_start: 0.8390 (mmm) cc_final: 0.7889 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 116
  average time/residue: 0.2582
  time to fit residues: 38.9112
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  : 0.942 
-------------------------------------------------------------------------------
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  185 LEU
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:   40.0000
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 88 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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**
** B  82 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 = 0.3689 r_free = 0.3689 target = 0.078488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.052061 restraints weight = 42469.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.054637 restraints weight = 18340.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.056291 restraints weight = 10964.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    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 = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8213  Z= 0.229
  Angle     :  0.720   9.739  11203  Z= 0.370
  Chirality :  0.045   0.156   1262
  Planarity :  0.005   0.073   1425
  Dihedral  :  6.493  41.131   1210
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.43 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.97 %
    Favored  : 77.89 %
  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: -2.17 (0.55), residues: 63
  sheet: -1.03 (0.27), residues: 384
  loop : -1.79 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.040   0.002   PHE E 497 
 TYR   0.033   0.002   TYR E 495 
 ARG   0.003   0.000   ARG B  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       1.47633 (    3)
  link_ALPHA1-6        : bond        0.01060 (    1)
  link_ALPHA1-6        : angle       1.62441 (    3)
  link_BETA1-4         : bond        0.00646 (    2)
  link_BETA1-4         : angle       3.15852 (    6)
  hydrogen bonds       : bond        0.03737 (  205)
  hydrogen bonds       : angle       7.19295 (  531)
  SS BOND              : bond        0.00403 (   10)
  SS BOND              : angle       1.95489 (   20)
  covalent geometry    : bond        0.00492 ( 8199)
  covalent geometry    : angle       0.71156 (11171)

*********************** 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
  118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.953 
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: 0.9090 (mptt) cc_final: 0.8753 (tptt)
REVERT: E  406 GLU cc_start: 0.9465 (mt-10) cc_final: 0.8693 (mp0)
REVERT: E  515 PHE cc_start: 0.9420 (m-80) cc_final: 0.9027 (m-80)
REVERT: D    4 MET cc_start: 0.7976 (mmm) cc_final: 0.7715 (mmm)
REVERT: D   93 ASN cc_start: 0.8867 (m-40) cc_final: 0.8342 (t0)
REVERT: D  105 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7786 (mp0)
REVERT: D  142 ARG cc_start: 0.8795 (tmt170) cc_final: 0.8294 (ttp80)
REVERT: B   32 TYR cc_start: 0.8406 (m-80) cc_final: 0.7817 (m-10)
REVERT: B   62 ASP cc_start: 0.8564 (t0) cc_final: 0.8321 (t0)
REVERT: B  199 GLN cc_start: 0.8381 (mt0) cc_final: 0.8077 (tp40)
REVERT: B  206 ASN cc_start: 0.7245 (t0) cc_final: 0.6908 (t0)
REVERT: B  216 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8548 (ttpp)
REVERT: C  147 CYS cc_start: 0.7874 (p) cc_final: 0.6797 (m)
REVERT: A   38 TYR cc_start: 0.8255 (m-80) cc_final: 0.7648 (m-80)
REVERT: A   49 MET cc_start: 0.8347 (mmm) cc_final: 0.7837 (mmm)
  outliers start: 27
  outliers final: 25
  residues processed: 114
  average time/residue: 0.2909
  time to fit residues: 43.3585
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
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   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  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  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:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 76 optimal weight:   50.0000
   chunk 1 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.080506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.052444 restraints weight = 66389.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.055743 restraints weight = 22897.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.057739 restraints weight = 12467.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8213  Z= 0.168
  Angle     :  0.691   9.986  11203  Z= 0.353
  Chirality :  0.044   0.166   1262
  Planarity :  0.005   0.052   1425
  Dihedral  :  6.049  46.373   1210
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.36 %
    Favored  : 91.35 %
  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: -2.06 (0.27), residues: 1030
  helix: -2.13 (0.55), residues: 65
  sheet: -0.84 (0.28), residues: 381
  loop : -1.65 (0.26), residues: 584

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   0.032   0.002   PHE E 497 
 TYR   0.027   0.002   TYR E 495 
 ARG   0.003   0.000   ARG C  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00125 (    1)
  link_NAG-ASN         : angle       1.35863 (    3)
  link_ALPHA1-6        : bond        0.01233 (    1)
  link_ALPHA1-6        : angle       1.43995 (    3)
  link_BETA1-4         : bond        0.00668 (    2)
  link_BETA1-4         : angle       2.80117 (    6)
  hydrogen bonds       : bond        0.03310 (  205)
  hydrogen bonds       : angle       6.97827 (  531)
  SS BOND              : bond        0.00321 (   10)
  SS BOND              : angle       1.89771 (   20)
  covalent geometry    : bond        0.00368 ( 8199)
  covalent geometry    : angle       0.68377 (11171)

*********************** 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
  123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 1.007 
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: 0.9075 (mptt) cc_final: 0.8747 (tptt)
REVERT: E  406 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8688 (mp0)
REVERT: E  465 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7318 (tt0)
REVERT: E  515 PHE cc_start: 0.9387 (m-80) cc_final: 0.9032 (m-80)
REVERT: D   93 ASN cc_start: 0.8883 (m-40) cc_final: 0.8417 (t0)
REVERT: D  105 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7794 (mp0)
REVERT: D  142 ARG cc_start: 0.8760 (tmt170) cc_final: 0.8250 (ttp80)
REVERT: B   32 TYR cc_start: 0.8386 (m-80) cc_final: 0.7785 (m-10)
REVERT: B   62 ASP cc_start: 0.8557 (t0) cc_final: 0.8313 (t0)
REVERT: B  199 GLN cc_start: 0.8429 (mt0) cc_final: 0.8128 (tp40)
REVERT: B  206 ASN cc_start: 0.7259 (t0) cc_final: 0.6918 (t0)
REVERT: B  216 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8570 (ttpp)
REVERT: C  129 PHE cc_start: 0.8198 (m-10) cc_final: 0.7992 (m-10)
REVERT: C  147 CYS cc_start: 0.7752 (p) cc_final: 0.6606 (m)
REVERT: A   38 TYR cc_start: 0.8124 (m-80) cc_final: 0.7534 (m-80)
REVERT: A   49 MET cc_start: 0.8379 (mmm) cc_final: 0.7837 (mmm)
  outliers start: 29
  outliers final: 22
  residues processed: 118
  average time/residue: 0.2664
  time to fit residues: 41.7129
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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 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  101 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0010
   chunk 97 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 84 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.7792

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.081221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.054338 restraints weight = 44906.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.057165 restraints weight = 18587.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.058956 restraints weight = 10996.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8213  Z= 0.151
  Angle     :  0.697  10.120  11203  Z= 0.353
  Chirality :  0.045   0.156   1262
  Planarity :  0.005   0.076   1425
  Dihedral  :  5.866  58.711   1210
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.26 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.98 %
    Favored  : 76.99 %
  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: -1.91 (0.27), residues: 1030
  helix: -1.98 (0.56), residues: 65
  sheet: -0.65 (0.29), residues: 367
  loop : -1.61 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 353 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.027   0.002   PHE E 497 
 TYR   0.026   0.002   TYR A  34 
 ARG   0.004   0.000   ARG C  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00122 (    1)
  link_NAG-ASN         : angle       1.40216 (    3)
  link_ALPHA1-6        : bond        0.00885 (    1)
  link_ALPHA1-6        : angle       1.24352 (    3)
  link_BETA1-4         : bond        0.00724 (    2)
  link_BETA1-4         : angle       2.64474 (    6)
  hydrogen bonds       : bond        0.03137 (  205)
  hydrogen bonds       : angle       6.82769 (  531)
  SS BOND              : bond        0.00339 (   10)
  SS BOND              : angle       1.82750 (   20)
  covalent geometry    : bond        0.00336 ( 8199)
  covalent geometry    : angle       0.69070 (11171)

*********************** 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
  124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 1.032 
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: 0.9072 (mptt) cc_final: 0.8761 (tptt)
REVERT: E  390 LEU cc_start: 0.7058 (tp) cc_final: 0.6723 (tt)
REVERT: E  406 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8643 (mp0)
REVERT: E  468 ILE cc_start: 0.9306 (pt) cc_final: 0.9028 (tp)
REVERT: E  515 PHE cc_start: 0.9387 (m-80) cc_final: 0.9053 (m-80)
REVERT: D   93 ASN cc_start: 0.8849 (m-40) cc_final: 0.8414 (t0)
REVERT: D  105 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7774 (mp0)
REVERT: D  142 ARG cc_start: 0.8734 (tmt170) cc_final: 0.8216 (ttp80)
REVERT: B   62 ASP cc_start: 0.8547 (t0) cc_final: 0.8290 (t0)
REVERT: B  199 GLN cc_start: 0.8441 (mt0) cc_final: 0.8129 (tp40)
REVERT: B  213 LYS cc_start: 0.9318 (mtpt) cc_final: 0.8838 (tptt)
REVERT: B  216 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8581 (ttpp)
REVERT: C  129 PHE cc_start: 0.8203 (m-10) cc_final: 0.7960 (m-10)
REVERT: C  147 CYS cc_start: 0.7802 (p) cc_final: 0.6733 (m)
REVERT: A   38 TYR cc_start: 0.8052 (m-80) cc_final: 0.7464 (m-80)
REVERT: A   49 MET cc_start: 0.8398 (mmm) cc_final: 0.7869 (mmm)
  outliers start: 26
  outliers final: 24
  residues processed: 119
  average time/residue: 0.2723
  time to fit residues: 43.0539
Evaluate side-chains
  112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
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   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   28 THR
Chi-restraints excluded: chain C residue   68 PHE
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  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:    2.9990
   chunk 98 optimal weight:    0.0470
   chunk 38 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 99 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0020
   chunk 20 optimal weight:    8.9990
   chunk 72 optimal weight:    7.9990
   chunk 60 optimal weight:    0.5980
   chunk 55 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    2.1290

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.080908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.054414 restraints weight = 42915.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.057157 restraints weight = 17951.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.058881 restraints weight = 10642.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    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 = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8213  Z= 0.170
  Angle     :  0.713   9.985  11203  Z= 0.364
  Chirality :  0.045   0.154   1262
  Planarity :  0.005   0.053   1425
  Dihedral  :  5.776  58.099   1210
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.26 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.76 %
    Favored  : 75.87 %
  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: -1.89 (0.27), residues: 1030
  helix: -1.95 (0.56), residues: 65
  sheet: -0.69 (0.28), residues: 375
  loop : -1.57 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.026   0.002   PHE E 497 
 TYR   0.024   0.002   TYR E 495 
 ARG   0.009   0.001   ARG B  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       1.53949 (    3)
  link_ALPHA1-6        : bond        0.00835 (    1)
  link_ALPHA1-6        : angle       1.33404 (    3)
  link_BETA1-4         : bond        0.00655 (    2)
  link_BETA1-4         : angle       2.42748 (    6)
  hydrogen bonds       : bond        0.03175 (  205)
  hydrogen bonds       : angle       6.73303 (  531)
  SS BOND              : bond        0.00326 (   10)
  SS BOND              : angle       1.85482 (   20)
  covalent geometry    : bond        0.00378 ( 8199)
  covalent geometry    : angle       0.70634 (11171)

*********************** 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
  120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.838 
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: 0.9073 (mptt) cc_final: 0.8777 (tptt)
REVERT: E  390 LEU cc_start: 0.7181 (tp) cc_final: 0.6845 (tt)
REVERT: E  406 GLU cc_start: 0.9414 (mt-10) cc_final: 0.8653 (mp0)
REVERT: E  468 ILE cc_start: 0.9309 (pt) cc_final: 0.9033 (tp)
REVERT: D   93 ASN cc_start: 0.8855 (m-40) cc_final: 0.8428 (t0)
REVERT: D  105 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7780 (mp0)
REVERT: D  142 ARG cc_start: 0.8745 (tmt170) cc_final: 0.8217 (ttp80)
REVERT: B   62 ASP cc_start: 0.8585 (t0) cc_final: 0.8326 (t0)
REVERT: B  199 GLN cc_start: 0.8370 (mt0) cc_final: 0.8067 (tp40)
REVERT: B  216 LYS cc_start: 0.9118 (ttmm) cc_final: 0.8580 (ttpp)
REVERT: C  129 PHE cc_start: 0.8182 (m-10) cc_final: 0.7917 (m-10)
REVERT: C  147 CYS cc_start: 0.7839 (p) cc_final: 0.6880 (m)
REVERT: A   38 TYR cc_start: 0.8019 (m-80) cc_final: 0.7453 (m-80)
REVERT: A   49 MET cc_start: 0.8389 (mmm) cc_final: 0.7853 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 115
  average time/residue: 0.2458
  time to fit residues: 37.6173
Evaluate side-chains
  107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
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   28 THR
Chi-restraints excluded: chain C residue   68 PHE
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
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:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 95 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    3.9388

-------------------------------------------------------------------------------
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**
** 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 = 0.3679 r_free = 0.3679 target = 0.077866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.052079 restraints weight = 35454.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.054415 restraints weight = 16545.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.055913 restraints weight = 10318.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8213  Z= 0.261
  Angle     :  0.776  11.129  11203  Z= 0.400
  Chirality :  0.046   0.189   1262
  Planarity :  0.006   0.079   1425
  Dihedral  :  6.047  58.443   1210
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 19.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.30 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.66 %
    Favored  : 75.65 %
  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: -2.12 (0.27), residues: 1030
  helix: -1.94 (0.56), residues: 65
  sheet: -0.99 (0.27), residues: 399
  loop : -1.64 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 110 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.031   0.002   PHE E 497 
 TYR   0.037   0.002   TYR A 176 
 ARG   0.008   0.001   ARG B  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00326 (    1)
  link_NAG-ASN         : angle       1.94328 (    3)
  link_ALPHA1-6        : bond        0.00925 (    1)
  link_ALPHA1-6        : angle       1.22137 (    3)
  link_BETA1-4         : bond        0.00553 (    2)
  link_BETA1-4         : angle       2.46290 (    6)
  hydrogen bonds       : bond        0.03736 (  205)
  hydrogen bonds       : angle       6.89311 (  531)
  SS BOND              : bond        0.00482 (   10)
  SS BOND              : angle       1.82086 (   20)
  covalent geometry    : bond        0.00566 ( 8199)
  covalent geometry    : angle       0.77026 (11171)

********************** 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
  111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.976 
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: E  386 LYS cc_start: 0.9086 (mptt) cc_final: 0.8802 (tptt)
REVERT: E  390 LEU cc_start: 0.7192 (tp) cc_final: 0.6869 (tt)
REVERT: E  406 GLU cc_start: 0.9458 (mt-10) cc_final: 0.8656 (mp0)
REVERT: E  468 ILE cc_start: 0.9301 (pt) cc_final: 0.9018 (tp)
REVERT: D   93 ASN cc_start: 0.8918 (m-40) cc_final: 0.8466 (t0)
REVERT: D  105 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7775 (mp0)
REVERT: D  142 ARG cc_start: 0.8771 (tmt170) cc_final: 0.8213 (ttp80)
REVERT: B   62 ASP cc_start: 0.8621 (t0) cc_final: 0.8376 (t0)
REVERT: B  199 GLN cc_start: 0.8380 (mt0) cc_final: 0.8080 (tp40)
REVERT: B  216 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8552 (ttpp)
REVERT: C  129 PHE cc_start: 0.8198 (m-10) cc_final: 0.7914 (m-10)
REVERT: C  147 CYS cc_start: 0.7838 (p) cc_final: 0.7013 (m)
REVERT: A   38 TYR cc_start: 0.8223 (m-80) cc_final: 0.7620 (m-80)
REVERT: A   49 MET cc_start: 0.8310 (mmm) cc_final: 0.7817 (mmm)
  outliers start: 23
  outliers final: 21
  residues processed: 107
  average time/residue: 0.3074
  time to fit residues: 43.2007
Evaluate side-chains
  106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  361 CYS
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   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
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:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.081199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.054258 restraints weight = 50858.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.057291 restraints weight = 19707.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.059149 restraints weight = 11211.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    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 = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8213  Z= 0.150
  Angle     :  0.735  10.370  11203  Z= 0.374
  Chirality :  0.045   0.194   1262
  Planarity :  0.005   0.055   1425
  Dihedral  :  5.907  59.668   1210
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.26 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.89 %
    Favored  : 75.31 %
  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: -1.84 (0.27), residues: 1030
  helix: -1.88 (0.57), residues: 65
  sheet: -0.68 (0.28), residues: 374
  loop : -1.51 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 152 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.026   0.002   PHE E 497 
 TYR   0.037   0.002   TYR A 176 
 ARG   0.007   0.001   ARG E 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00053 (    1)
  link_NAG-ASN         : angle       1.51902 (    3)
  link_ALPHA1-6        : bond        0.00853 (    1)
  link_ALPHA1-6        : angle       1.18963 (    3)
  link_BETA1-4         : bond        0.00638 (    2)
  link_BETA1-4         : angle       2.06355 (    6)
  hydrogen bonds       : bond        0.03103 (  205)
  hydrogen bonds       : angle       6.68502 (  531)
  SS BOND              : bond        0.00397 (   10)
  SS BOND              : angle       1.67386 (   20)
  covalent geometry    : bond        0.00337 ( 8199)
  covalent geometry    : angle       0.73009 (11171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4814.38 seconds
wall clock time: 86 minutes 46.83 seconds (5206.83 seconds total)