Starting phenix.real_space_refine
on Tue Mar  3 21:56:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ezm_31389/03_2026/7ezm_31389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ezm_31389/03_2026/7ezm_31389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2026/7ezm_31389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2026/7ezm_31389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2026/7ezm_31389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2026/7ezm_31389.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      69      5.16       5
     C    5748      2.51       5
     N    1524      2.21       5
     O    1667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9008
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1850
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2561
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2362
          Classifications: {'peptide': 304}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 12, 'TRANS': 291}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 44
    Chain: "G"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 421
          Classifications: {'peptide': 59}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "H"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1736
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "P"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYS:plan-2': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 1.89, per 1000 atoms: 0.21
  Number of scatterers: 9008
  At special positions: 0
  Unit cell: (104.5, 120.175, 121.22, 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      69     16.00
     O    1667      8.00
     N    1524      7.00
     C    5748      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 114 " - pdb=" SG  CYS D 196 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 383.2 milliseconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      40.1% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 38
    Processing helix  chain 'A' and resid 51 through 63
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.595A  pdb=" N   ILE A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 246 through 261
    Processing helix  chain 'A' and resid 262 through 266
      removed outlier: 3.550A  pdb=" N   GLN A 265 " --> pdb=" O   PRO A 262 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ASN A 266 " --> pdb=" O   TRP A 263 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 262 through 266'
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'A' and resid 287 through 291
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 4.209A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'D' and resid 39 through 69
    Processing helix  chain 'D' and resid 70 through 73
    Processing helix  chain 'D' and resid 74 through 105
      Proline residue:  D  96  - end of helix
      Proline residue:  D 101  - end of helix
    Processing helix  chain 'D' and resid 110 through 145
    Processing helix  chain 'D' and resid 147 through 152
    Processing helix  chain 'D' and resid 154 through 173
    Processing helix  chain 'D' and resid 174 through 180
      removed outlier: 3.595A  pdb=" N   ILE D 178 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 217
    Processing helix  chain 'D' and resid 218 through 248
    Processing helix  chain 'D' and resid 301 through 339
      Proline residue:  D 328  - end of helix
    Processing helix  chain 'D' and resid 339 through 348
    Processing helix  chain 'D' and resid 349 through 371
      removed outlier: 4.019A  pdb=" N   SER D 363 " --> pdb=" O   SER D 359 " (cutoff:3.500A)
      Proline residue:  D 367  - end of helix
    Processing helix  chain 'D' and resid 374 through 383
    Processing helix  chain 'G' and resid 9 through 25
      removed outlier: 3.849A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 52 through 56
      removed outlier: 4.106A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196
      removed outlier: 6.662A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.882A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.675A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.354A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.814A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.649A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.827A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 186
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.063A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.507A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2088
        1.33 -     1.46: 2829
        1.46 -     1.60: 4172
        1.60 -     1.73: 1
        1.73 -     1.86: 106
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" O1  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.462  1.636 -0.174 2.00e-02 2.50e+03 7.56e+01
  bond pdb=" OH  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.526  0.153 2.00e-02 2.50e+03 5.81e+01
  bond pdb=" CA  SER B 281 "
       pdb=" CB  SER B 281 "
    ideal  model  delta    sigma   weight residual
    1.532  1.465  0.066 1.78e-02 3.16e+03 1.39e+01
  bond pdb=" N   VAL A 240 "
       pdb=" CA  VAL A 240 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.60e+00
  bond pdb=" N   GLY B  41 "
       pdb=" CA  GLY B  41 "
    ideal  model  delta    sigma   weight residual
    1.448  1.492 -0.044 1.88e-02 2.83e+03 5.56e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 11457
        1.81 -     3.62: 914
        3.62 -     5.43: 91
        5.43 -     7.24: 18
        7.24 -     9.05: 4
  Bond angle restraints: 12484
  Sorted by residual:
  angle pdb=" C   ARG D 139 "
        pdb=" CA  ARG D 139 "
        pdb=" CB  ARG D 139 "
      ideal   model   delta    sigma   weight residual
     110.68  118.72   -8.04 1.70e+00 3.46e-01 2.23e+01
  angle pdb=" C   ARG D 345 "
        pdb=" CA  ARG D 345 "
        pdb=" CB  ARG D 345 "
      ideal   model   delta    sigma   weight residual
     110.88  103.83    7.05 1.57e+00 4.06e-01 2.02e+01
  angle pdb=" N   VAL A 238 "
        pdb=" CA  VAL A 238 "
        pdb=" C   VAL A 238 "
      ideal   model   delta    sigma   weight residual
     109.20  102.41    6.79 1.55e+00 4.16e-01 1.92e+01
  angle pdb=" N   ALA H 136 "
        pdb=" CA  ALA H 136 "
        pdb=" C   ALA H 136 "
      ideal   model   delta    sigma   weight residual
     113.02  107.99    5.03 1.20e+00 6.94e-01 1.75e+01
  angle pdb=" CA  VAL A 238 "
        pdb=" C   VAL A 238 "
        pdb=" O   VAL A 238 "
      ideal   model   delta    sigma   weight residual
     121.92  117.04    4.88 1.17e+00 7.31e-01 1.74e+01
  ... (remaining 12479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 4939
       16.36 -    32.71: 413
       32.71 -    49.06: 76
       49.06 -    65.42: 22
       65.42 -    81.77: 5
  Dihedral angle restraints: 5455
    sinusoidal: 2051
      harmonic: 3404
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.95  -63.95     1      1.00e+01 1.00e-02 5.38e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.59   28.41     0      5.00e+00 4.00e-02 3.23e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.84   27.16     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 5452 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1137
       0.081 -    0.163: 272
       0.163 -    0.244: 23
       0.244 -    0.325: 3
       0.325 -    0.407: 2
  Chirality restraints: 1437
  Sorted by residual:
  chirality pdb=" CA  ARG A 210 "
            pdb=" N   ARG A 210 "
            pdb=" C   ARG A 210 "
            pdb=" CB  ARG A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.92   -0.41 2.00e-01 2.50e+01 4.14e+00
  chirality pdb=" CA  ARG D 345 "
            pdb=" N   ARG D 345 "
            pdb=" C   ARG D 345 "
            pdb=" CB  ARG D 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" CG  LEU A 316 "
            pdb=" CB  LEU A 316 "
            pdb=" CD1 LEU A 316 "
            pdb=" CD2 LEU A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1434 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 313 "    0.048 9.50e-02 1.11e+02   4.23e-02 1.69e+01
        pdb=" NE  ARG D 313 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 313 "    0.070 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 313 "   -0.024 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 313 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D 367 "   -0.020 2.00e-02 2.50e+03   4.08e-02 1.67e+01
        pdb=" C   PRO D 367 "    0.071 2.00e-02 2.50e+03
        pdb=" O   PRO D 367 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ILE D 368 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 202 "   -0.006 9.50e-02 1.11e+02   3.17e-02 1.25e+01
        pdb=" NE  ARG A 202 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 202 "   -0.061 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 202 "    0.021 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 202 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1292
        2.76 -     3.30: 9206
        3.30 -     3.83: 15416
        3.83 -     4.37: 19126
        4.37 -     4.90: 32178
  Nonbonded interactions: 77218
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 356 "
            pdb=" OE1 GLN D 153 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   TYR D 360 "
            pdb=" OG  SER D 363 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   MET D  72 "
            pdb=" ND2 ASN D  77 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN D  98 "
            pdb=" OH  TYR D 360 "
     model   vdw
     2.260 3.040
  ... (remaining 77213 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.980
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
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      :  0.011   0.174   9200  Z= 0.561
  Angle     :  1.074   9.054  12492  Z= 0.645
  Chirality :  0.068   0.407   1437
  Planarity :  0.009   0.102   1576
  Dihedral  : 13.160  81.772   3241
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  3.34 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.23), residues: 1150
  helix: -0.43 (0.23), residues: 404
  sheet: -0.10 (0.30), residues: 278
  loop : -0.83 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.071   0.009   ARG D 313 
 TYR   0.046   0.009   TYR H 175 
 PHE   0.025   0.006   PHE B 241 
 TRP   0.037   0.008   TRP B  82 
 HIS   0.019   0.006   HIS D 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.01068 ( 9196)
  covalent geometry    : angle       1.07377 (12484)
  SS BOND              : bond        0.01126 (    4)
  SS BOND              : angle       1.86097 (    8)
  hydrogen bonds       : bond        0.16802 (  482)
  hydrogen bonds       : angle       7.01862 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 308
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.7426 (p) cc_final: 0.6994 (p)
REVERT: A    9 ASP cc_start: 0.6886 (m-30) cc_final: 0.6420 (m-30)
REVERT: A   39 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6529 (mt-10)
REVERT: A  237 GLN cc_start: 0.7324 (mt0) cc_final: 0.7086 (mt0)
REVERT: A  275 LYS cc_start: 0.7832 (mttt) cc_final: 0.7625 (mttt)
REVERT: B   67 SER cc_start: 0.7986 (m) cc_final: 0.7688 (t)
REVERT: B   74 SER cc_start: 0.7782 (t) cc_final: 0.7454 (t)
REVERT: B   98 SER cc_start: 0.7826 (p) cc_final: 0.7445 (t)
REVERT: B  118 ASP cc_start: 0.6246 (p0) cc_final: 0.5987 (p0)
REVERT: B  184 THR cc_start: 0.8506 (p) cc_final: 0.8296 (t)
REVERT: B  220 GLN cc_start: 0.8247 (mt0) cc_final: 0.7890 (mt0)
REVERT: B  221 THR cc_start: 0.7915 (m) cc_final: 0.7714 (t)
REVERT: B  277 SER cc_start: 0.8359 (t) cc_final: 0.8149 (t)
REVERT: B  334 SER cc_start: 0.7768 (m) cc_final: 0.7554 (p)
REVERT: D   76 THR cc_start: 0.7375 (m) cc_final: 0.7143 (m)
REVERT: D  111 SER cc_start: 0.8252 (t) cc_final: 0.8007 (p)
REVERT: H  141 THR cc_start: 0.7753 (m) cc_final: 0.7420 (p)
REVERT: H  180 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7688 (mtt180)
  outliers start: 9
  outliers final: 4
  residues processed: 315
  average time/residue: 0.5020
  time to fit residues: 169.0378
Evaluate side-chains
  277 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 273
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ASN
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain H residue  135 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 132 ASN
D 131 ASN
D 374 ASN
H 142 GLN
H 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.136050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.121942 restraints weight = 12317.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.93
r_work: 0.3358 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9200  Z= 0.166
  Angle     :  0.626   6.863  12492  Z= 0.331
  Chirality :  0.045   0.156   1437
  Planarity :  0.005   0.042   1576
  Dihedral  :  6.920  71.910   1271
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 13.26 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.25), residues: 1150
  helix:  1.32 (0.26), residues: 409
  sheet: -0.24 (0.29), residues: 282
  loop :  0.01 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 345 
 TYR   0.014   0.002   TYR H 190 
 PHE   0.030   0.002   PHE A  55 
 TRP   0.025   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9196)
  covalent geometry    : angle       0.62309 (12484)
  SS BOND              : bond        0.01168 (    4)
  SS BOND              : angle       2.51497 (    8)
  hydrogen bonds       : bond        0.04311 (  482)
  hydrogen bonds       : angle       5.17247 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 274
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8234 (p) cc_final: 0.7933 (p)
REVERT: A   39 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7406 (mt-10)
REVERT: A  201 PHE cc_start: 0.8329 (m-80) cc_final: 0.7834 (m-80)
REVERT: A  212 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7687 (mt-10)
REVERT: A  276 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7411 (ptpp)
REVERT: A  290 ASP cc_start: 0.7625 (m-30) cc_final: 0.7388 (m-30)
REVERT: B   52 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7537 (ptp90)
REVERT: B   68 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7763 (ttt180)
REVERT: B   98 SER cc_start: 0.7741 (p) cc_final: 0.7367 (t)
REVERT: B  170 ASP cc_start: 0.7755 (t70) cc_final: 0.7368 (OUTLIER)
REVERT: B  186 ASP cc_start: 0.7060 (t0) cc_final: 0.6819 (t0)
REVERT: B  212 ASP cc_start: 0.7749 (t70) cc_final: 0.7458 (t0)
REVERT: B  214 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7509 (mtm-85)
REVERT: B  256 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8271 (mtm180)
REVERT: B  268 ASN cc_start: 0.7639 (p0) cc_final: 0.7418 (p0)
REVERT: B  271 CYS cc_start: 0.7870 (m) cc_final: 0.7546 (p)
REVERT: D  126 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (m)
REVERT: D  202 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7532 (p0)
REVERT: D  308 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7982 (mttm)
REVERT: D  344 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7621 (mt-10)
REVERT: H   34 MET cc_start: 0.8549 (mmt) cc_final: 0.8322 (mmm)
REVERT: H   68 PHE cc_start: 0.7296 (m-10) cc_final: 0.6732 (m-80)
REVERT: H   78 THR cc_start: 0.8444 (t) cc_final: 0.7839 (m)
REVERT: H  141 THR cc_start: 0.8019 (m) cc_final: 0.7624 (p)
REVERT: H  180 ARG cc_start: 0.8366 (mtt180) cc_final: 0.8030 (mtt180)
REVERT: P    8 PHE cc_start: 0.8429 (m-10) cc_final: 0.8183 (m-10)
  outliers start: 46
  outliers final: 22
  residues processed: 292
  average time/residue: 0.5306
  time to fit residues: 165.4084
Evaluate side-chains
  263 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 239
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  126 SER
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  202 ASN
Chi-restraints excluded: chain D residue  304 ASN
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0470
   chunk 75 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0170
   chunk 57 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 111 optimal weight:    0.7980
   chunk 45 optimal weight:    0.4980
   chunk 89 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0060
   overall best weight:    0.2532

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
D  77 ASN
D 374 ASN
G  18 GLN
H 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.123381 restraints weight = 12270.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.94
r_work: 0.3390 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9200  Z= 0.115
  Angle     :  0.556   7.714  12492  Z= 0.292
  Chirality :  0.042   0.143   1437
  Planarity :  0.004   0.042   1576
  Dihedral  :  5.466  71.250   1263
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 17.33 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.25), residues: 1150
  helix:  1.68 (0.26), residues: 417
  sheet: -0.17 (0.29), residues: 280
  loop :  0.06 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 129 
 TYR   0.016   0.001   TYR D 179 
 PHE   0.032   0.001   PHE A  55 
 TRP   0.023   0.002   TRP B 339 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9196)
  covalent geometry    : angle       0.55452 (12484)
  SS BOND              : bond        0.00550 (    4)
  SS BOND              : angle       1.91874 (    8)
  hydrogen bonds       : bond        0.03668 (  482)
  hydrogen bonds       : angle       4.79958 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 261
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8287 (p) cc_final: 0.7925 (p)
REVERT: A    9 ASP cc_start: 0.7960 (m-30) cc_final: 0.7621 (m-30)
REVERT: A   39 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7395 (mt-10)
REVERT: A  201 PHE cc_start: 0.8378 (m-80) cc_final: 0.7679 (m-80)
REVERT: A  212 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7783 (mt-10)
REVERT: A  276 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7449 (ptpp)
REVERT: A  290 ASP cc_start: 0.7666 (m-30) cc_final: 0.7413 (m-30)
REVERT: A  307 GLU cc_start: 0.7960 (tp30) cc_final: 0.7699 (tp30)
REVERT: A  355 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6957 (mm-30)
REVERT: B   33 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7575 (mt)
REVERT: B   52 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7303 (mtp85)
REVERT: B   98 SER cc_start: 0.7652 (p) cc_final: 0.7324 (t)
REVERT: B  137 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7838 (tpp-160)
REVERT: B  165 THR cc_start: 0.7970 (p) cc_final: 0.6652 (m)
REVERT: B  170 ASP cc_start: 0.7743 (t70) cc_final: 0.7317 (t0)
REVERT: B  212 ASP cc_start: 0.7697 (t70) cc_final: 0.7429 (t0)
REVERT: B  214 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7579 (mtm180)
REVERT: B  256 ARG cc_start: 0.8654 (mtm180) cc_final: 0.8383 (mtm180)
REVERT: B  268 ASN cc_start: 0.7645 (p0) cc_final: 0.7416 (p0)
REVERT: B  271 CYS cc_start: 0.7997 (m) cc_final: 0.7653 (p)
REVERT: B  274 THR cc_start: 0.7774 (m) cc_final: 0.7547 (p)
REVERT: B  289 TYR cc_start: 0.7340 (m-10) cc_final: 0.6880 (m-80)
REVERT: D  126 SER cc_start: 0.8610 (t) cc_final: 0.8368 (m)
REVERT: D  202 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7638 (p0)
REVERT: D  308 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7996 (mttp)
REVERT: D  344 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: H   34 MET cc_start: 0.8527 (mmt) cc_final: 0.8303 (mmm)
REVERT: H   63 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8126 (t)
REVERT: H  141 THR cc_start: 0.7981 (m) cc_final: 0.7623 (p)
  outliers start: 38
  outliers final: 22
  residues processed: 279
  average time/residue: 0.5458
  time to fit residues: 162.6927
Evaluate side-chains
  266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 240
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  202 ASN
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  304 ASN
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0010
   chunk 104 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.136635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.122319 restraints weight = 12335.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.96
r_work: 0.3349 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9200  Z= 0.136
  Angle     :  0.556   6.842  12492  Z= 0.291
  Chirality :  0.042   0.160   1437
  Planarity :  0.004   0.041   1576
  Dihedral  :  5.252  69.832   1262
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.79 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.25), residues: 1150
  helix:  1.90 (0.25), residues: 410
  sheet: -0.26 (0.29), residues: 285
  loop :  0.04 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.016   0.001   TYR D 179 
 PHE   0.023   0.002   PHE A  55 
 TRP   0.019   0.002   TRP B 339 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9196)
  covalent geometry    : angle       0.55369 (12484)
  SS BOND              : bond        0.00728 (    4)
  SS BOND              : angle       2.05783 (    8)
  hydrogen bonds       : bond        0.03677 (  482)
  hydrogen bonds       : angle       4.68827 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 245
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8432 (p) cc_final: 0.8175 (p)
REVERT: A    9 ASP cc_start: 0.7928 (m-30) cc_final: 0.7638 (m-30)
REVERT: A   39 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7358 (mt-10)
REVERT: A  201 PHE cc_start: 0.8425 (m-80) cc_final: 0.7778 (m-80)
REVERT: A  276 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7474 (ptpp)
REVERT: A  290 ASP cc_start: 0.7689 (m-30) cc_final: 0.7420 (m-30)
REVERT: A  307 GLU cc_start: 0.8075 (tp30) cc_final: 0.7729 (tp30)
REVERT: A  322 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7748 (ttmm)
REVERT: B   52 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7328 (mtp85)
REVERT: B   87 THR cc_start: 0.8064 (m) cc_final: 0.7810 (t)
REVERT: B   98 SER cc_start: 0.7852 (p) cc_final: 0.7476 (t)
REVERT: B  165 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.6644 (m)
REVERT: B  170 ASP cc_start: 0.7893 (t70) cc_final: 0.7450 (t0)
REVERT: B  212 ASP cc_start: 0.7648 (t70) cc_final: 0.7426 (t0)
REVERT: B  268 ASN cc_start: 0.7710 (p0) cc_final: 0.7507 (p0)
REVERT: B  271 CYS cc_start: 0.7993 (m) cc_final: 0.7707 (p)
REVERT: B  274 THR cc_start: 0.7854 (m) cc_final: 0.7611 (p)
REVERT: B  289 TYR cc_start: 0.7485 (m-10) cc_final: 0.7114 (m-80)
REVERT: D   74 THR cc_start: 0.8055 (t) cc_final: 0.7601 (p)
REVERT: D   75 VAL cc_start: 0.8073 (p) cc_final: 0.7509 (t)
REVERT: D  126 SER cc_start: 0.8636 (t) cc_final: 0.8384 (m)
REVERT: D  202 ASN cc_start: 0.8073 (p0) cc_final: 0.7805 (p0)
REVERT: D  241 LYS cc_start: 0.7978 (mttp) cc_final: 0.7755 (mttp)
REVERT: D  336 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7886 (ttt180)
REVERT: H   63 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (t)
REVERT: H  141 THR cc_start: 0.8012 (m) cc_final: 0.7630 (p)
REVERT: P    8 PHE cc_start: 0.8405 (m-10) cc_final: 0.8184 (m-10)
  outliers start: 35
  outliers final: 15
  residues processed: 259
  average time/residue: 0.5438
  time to fit residues: 150.1997
Evaluate side-chains
  250 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 231
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 30 optimal weight:    0.1980
   chunk 76 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.134463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.120298 restraints weight = 12350.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.94
r_work: 0.3334 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9200  Z= 0.150
  Angle     :  0.562   9.155  12492  Z= 0.290
  Chirality :  0.042   0.146   1437
  Planarity :  0.004   0.040   1576
  Dihedral  :  5.166  70.240   1262
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 19.10 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.25), residues: 1150
  helix:  1.98 (0.26), residues: 411
  sheet: -0.13 (0.29), residues: 280
  loop : -0.05 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  38 
 TYR   0.016   0.001   TYR D 179 
 PHE   0.026   0.002   PHE A  55 
 TRP   0.017   0.001   TRP B 339 
 HIS   0.004   0.001   HIS D 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9196)
  covalent geometry    : angle       0.55981 (12484)
  SS BOND              : bond        0.00685 (    4)
  SS BOND              : angle       1.99286 (    8)
  hydrogen bonds       : bond        0.03667 (  482)
  hydrogen bonds       : angle       4.63629 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 243
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8462 (p) cc_final: 0.8209 (p)
REVERT: A    9 ASP cc_start: 0.7896 (m-30) cc_final: 0.7617 (m-30)
REVERT: A   39 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7330 (mt-10)
REVERT: A   41 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8249 (mttm)
REVERT: A  201 PHE cc_start: 0.8478 (m-80) cc_final: 0.7822 (m-80)
REVERT: A  290 ASP cc_start: 0.7675 (m-30) cc_final: 0.7328 (m-30)
REVERT: A  307 GLU cc_start: 0.8069 (tp30) cc_final: 0.7745 (tp30)
REVERT: A  322 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7777 (ttmm)
REVERT: A  326 SER cc_start: 0.8628 (p) cc_final: 0.8420 (t)
REVERT: B   33 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7654 (mt)
REVERT: B   37 ILE cc_start: 0.7911 (mm) cc_final: 0.7686 (tt)
REVERT: B   52 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7337 (mtp85)
REVERT: B   87 THR cc_start: 0.8021 (m) cc_final: 0.7697 (t)
REVERT: B   98 SER cc_start: 0.7982 (p) cc_final: 0.7625 (t)
REVERT: B  165 THR cc_start: 0.7935 (p) cc_final: 0.7712 (p)
REVERT: B  170 ASP cc_start: 0.7919 (t70) cc_final: 0.7498 (t0)
REVERT: B  212 ASP cc_start: 0.7667 (t70) cc_final: 0.7438 (t0)
REVERT: B  227 SER cc_start: 0.8581 (m) cc_final: 0.8105 (t)
REVERT: B  268 ASN cc_start: 0.7830 (p0) cc_final: 0.7599 (OUTLIER)
REVERT: B  271 CYS cc_start: 0.8062 (m) cc_final: 0.7771 (p)
REVERT: B  274 THR cc_start: 0.7809 (m) cc_final: 0.7589 (p)
REVERT: B  289 TYR cc_start: 0.7616 (m-10) cc_final: 0.7294 (m-80)
REVERT: D   74 THR cc_start: 0.8060 (t) cc_final: 0.7705 (p)
REVERT: D   75 VAL cc_start: 0.8130 (p) cc_final: 0.7645 (t)
REVERT: D  126 SER cc_start: 0.8626 (t) cc_final: 0.8398 (m)
REVERT: D  202 ASN cc_start: 0.8130 (p0) cc_final: 0.7904 (p0)
REVERT: D  329 ILE cc_start: 0.8454 (tp) cc_final: 0.8243 (tt)
REVERT: D  336 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7884 (ttt180)
REVERT: H   30 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.8190 (t)
REVERT: H   63 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8156 (t)
  outliers start: 47
  outliers final: 24
  residues processed: 271
  average time/residue: 0.4981
  time to fit residues: 144.7035
Evaluate side-chains
  264 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 237
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   23 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0040
   chunk 25 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0170
   chunk 106 optimal weight:    0.4980
   chunk 34 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0010
   chunk 110 optimal weight:    5.9990
   overall best weight:    0.2636

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.136013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.121541 restraints weight = 12164.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.95
r_work: 0.3364 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9200  Z= 0.109
  Angle     :  0.538   8.831  12492  Z= 0.277
  Chirality :  0.041   0.163   1437
  Planarity :  0.004   0.039   1576
  Dihedral  :  5.066  70.683   1262
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 21.19 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1150
  helix:  2.09 (0.26), residues: 411
  sheet: -0.16 (0.29), residues: 291
  loop :  0.03 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  38 
 TYR   0.016   0.001   TYR D 179 
 PHE   0.025   0.001   PHE A  55 
 TRP   0.017   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9196)
  covalent geometry    : angle       0.53675 (12484)
  SS BOND              : bond        0.00795 (    4)
  SS BOND              : angle       1.71556 (    8)
  hydrogen bonds       : bond        0.03445 (  482)
  hydrogen bonds       : angle       4.53546 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 248
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8443 (p) cc_final: 0.8198 (p)
REVERT: A    9 ASP cc_start: 0.7870 (m-30) cc_final: 0.7619 (m-30)
REVERT: A   10 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8095 (mtmm)
REVERT: A   39 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7277 (mt-10)
REVERT: A   41 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8235 (mttm)
REVERT: A  201 PHE cc_start: 0.8470 (m-80) cc_final: 0.7667 (m-80)
REVERT: A  290 ASP cc_start: 0.7676 (m-30) cc_final: 0.7323 (m-30)
REVERT: A  307 GLU cc_start: 0.8068 (tp30) cc_final: 0.7755 (tp30)
REVERT: A  322 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7721 (ttmm)
REVERT: A  326 SER cc_start: 0.8627 (p) cc_final: 0.8425 (t)
REVERT: A  341 PHE cc_start: 0.8585 (t80) cc_final: 0.8142 (t80)
REVERT: B   33 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7633 (mt)
REVERT: B   52 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7293 (mtp85)
REVERT: B   87 THR cc_start: 0.7951 (m) cc_final: 0.7621 (t)
REVERT: B   98 SER cc_start: 0.7876 (p) cc_final: 0.7526 (t)
REVERT: B  161 SER cc_start: 0.7815 (p) cc_final: 0.7607 (m)
REVERT: B  165 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.6412 (m)
REVERT: B  170 ASP cc_start: 0.7910 (t70) cc_final: 0.7469 (t0)
REVERT: B  212 ASP cc_start: 0.7624 (t70) cc_final: 0.7412 (t0)
REVERT: B  220 GLN cc_start: 0.8370 (mt0) cc_final: 0.8076 (mt0)
REVERT: B  227 SER cc_start: 0.8553 (m) cc_final: 0.8087 (t)
REVERT: B  268 ASN cc_start: 0.7744 (p0) cc_final: 0.7506 (OUTLIER)
REVERT: B  271 CYS cc_start: 0.8068 (m) cc_final: 0.7782 (p)
REVERT: B  289 TYR cc_start: 0.7511 (m-10) cc_final: 0.7216 (m-80)
REVERT: D   74 THR cc_start: 0.8025 (t) cc_final: 0.7691 (p)
REVERT: D   75 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7592 (t)
REVERT: D  126 SER cc_start: 0.8639 (t) cc_final: 0.8396 (m)
REVERT: D  161 VAL cc_start: 0.8068 (t) cc_final: 0.7794 (t)
REVERT: D  170 PHE cc_start: 0.6859 (m-10) cc_final: 0.6507 (m-10)
REVERT: D  202 ASN cc_start: 0.8138 (p0) cc_final: 0.7901 (p0)
REVERT: D  213 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8069 (mp)
REVERT: D  336 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7835 (ttt180)
REVERT: D  344 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7522 (mt-10)
REVERT: D  365 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7453 (m)
REVERT: H   30 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.8190 (t)
REVERT: H   63 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8133 (t)
REVERT: H   67 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7792 (ttp80)
REVERT: H  199 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8040 (m)
  outliers start: 37
  outliers final: 18
  residues processed: 265
  average time/residue: 0.5988
  time to fit residues: 168.5838
Evaluate side-chains
  263 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 81 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0770
   chunk 85 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
D  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.130970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.116956 restraints weight = 12276.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.92
r_work: 0.3367 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9200  Z= 0.143
  Angle     :  0.553   9.108  12492  Z= 0.285
  Chirality :  0.042   0.178   1437
  Planarity :  0.004   0.039   1576
  Dihedral  :  5.092  69.534   1262
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 21.19 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.25), residues: 1150
  helix:  2.09 (0.26), residues: 411
  sheet: -0.28 (0.29), residues: 299
  loop :  0.01 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.018   0.001   TYR D 179 
 PHE   0.025   0.001   PHE A  55 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9196)
  covalent geometry    : angle       0.55140 (12484)
  SS BOND              : bond        0.00718 (    4)
  SS BOND              : angle       1.90025 (    8)
  hydrogen bonds       : bond        0.03593 (  482)
  hydrogen bonds       : angle       4.56284 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 252
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8521 (p) cc_final: 0.8235 (p)
REVERT: A    9 ASP cc_start: 0.7882 (m-30) cc_final: 0.7613 (m-30)
REVERT: A   10 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8128 (mtmm)
REVERT: A   39 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7118 (mt-10)
REVERT: A   41 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8254 (mttm)
REVERT: A  201 PHE cc_start: 0.8505 (m-80) cc_final: 0.7696 (m-80)
REVERT: A  202 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7984 (ttm-80)
REVERT: A  290 ASP cc_start: 0.7732 (m-30) cc_final: 0.7400 (m-30)
REVERT: A  307 GLU cc_start: 0.7989 (tp30) cc_final: 0.7686 (tp30)
REVERT: A  322 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7832 (ttmm)
REVERT: A  326 SER cc_start: 0.8643 (p) cc_final: 0.8442 (t)
REVERT: A  341 PHE cc_start: 0.8586 (t80) cc_final: 0.8090 (t80)
REVERT: B   33 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7711 (mt)
REVERT: B   37 ILE cc_start: 0.7887 (mm) cc_final: 0.7648 (tt)
REVERT: B   52 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7144 (mtt90)
REVERT: B   87 THR cc_start: 0.7925 (m) cc_final: 0.7617 (t)
REVERT: B   98 SER cc_start: 0.7985 (p) cc_final: 0.7631 (t)
REVERT: B  161 SER cc_start: 0.7852 (p) cc_final: 0.7592 (m)
REVERT: B  165 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.6461 (m)
REVERT: B  170 ASP cc_start: 0.7944 (t70) cc_final: 0.7513 (t0)
REVERT: B  212 ASP cc_start: 0.7672 (t70) cc_final: 0.7438 (t0)
REVERT: B  227 SER cc_start: 0.8575 (m) cc_final: 0.8147 (t)
REVERT: B  258 ASP cc_start: 0.7571 (m-30) cc_final: 0.7300 (m-30)
REVERT: B  271 CYS cc_start: 0.8049 (m) cc_final: 0.7776 (p)
REVERT: B  289 TYR cc_start: 0.7647 (m-10) cc_final: 0.7265 (m-80)
REVERT: D   74 THR cc_start: 0.7998 (t) cc_final: 0.7715 (p)
REVERT: D   75 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7623 (t)
REVERT: D  126 SER cc_start: 0.8658 (t) cc_final: 0.8433 (m)
REVERT: D  161 VAL cc_start: 0.8107 (t) cc_final: 0.7834 (t)
REVERT: D  202 ASN cc_start: 0.8220 (p0) cc_final: 0.7991 (p0)
REVERT: D  329 ILE cc_start: 0.8440 (tp) cc_final: 0.8226 (tt)
REVERT: D  336 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7841 (ttt180)
REVERT: D  344 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7543 (mt-10)
REVERT: H   30 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8189 (t)
REVERT: H   63 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8159 (t)
REVERT: H   67 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7882 (ttp80)
REVERT: H  199 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8109 (m)
  outliers start: 40
  outliers final: 21
  residues processed: 271
  average time/residue: 0.5265
  time to fit residues: 152.6347
Evaluate side-chains
  272 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 244
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.129133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115002 restraints weight = 12187.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.91
r_work: 0.3325 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9200  Z= 0.178
  Angle     :  0.598   9.107  12492  Z= 0.305
  Chirality :  0.044   0.202   1437
  Planarity :  0.004   0.038   1576
  Dihedral  :  5.221  69.580   1262
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 21.82 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.25), residues: 1150
  helix:  1.98 (0.26), residues: 411
  sheet: -0.17 (0.30), residues: 290
  loop : -0.05 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  38 
 TYR   0.015   0.002   TYR D 179 
 PHE   0.027   0.002   PHE A  55 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.004   0.001   HIS D 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9196)
  covalent geometry    : angle       0.59594 (12484)
  SS BOND              : bond        0.00768 (    4)
  SS BOND              : angle       1.88213 (    8)
  hydrogen bonds       : bond        0.03821 (  482)
  hydrogen bonds       : angle       4.65318 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 244
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8542 (p) cc_final: 0.8239 (p)
REVERT: A    9 ASP cc_start: 0.7891 (m-30) cc_final: 0.7616 (m-30)
REVERT: A   39 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7266 (mt-10)
REVERT: A   41 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8229 (mttm)
REVERT: A  201 PHE cc_start: 0.8565 (m-80) cc_final: 0.7693 (m-80)
REVERT: A  290 ASP cc_start: 0.7740 (m-30) cc_final: 0.7412 (m-30)
REVERT: A  307 GLU cc_start: 0.8037 (tp30) cc_final: 0.7703 (tp30)
REVERT: A  322 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7843 (ttmm)
REVERT: A  341 PHE cc_start: 0.8596 (t80) cc_final: 0.8109 (t80)
REVERT: B   37 ILE cc_start: 0.7908 (mm) cc_final: 0.7637 (tt)
REVERT: B   52 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7431 (mtp85)
REVERT: B   87 THR cc_start: 0.7987 (m) cc_final: 0.7691 (t)
REVERT: B   98 SER cc_start: 0.8167 (p) cc_final: 0.7860 (t)
REVERT: B  212 ASP cc_start: 0.7689 (t70) cc_final: 0.7456 (t0)
REVERT: B  221 THR cc_start: 0.8291 (t) cc_final: 0.8070 (m)
REVERT: B  258 ASP cc_start: 0.7488 (m-30) cc_final: 0.7173 (m-30)
REVERT: B  271 CYS cc_start: 0.8075 (m) cc_final: 0.7799 (p)
REVERT: B  289 TYR cc_start: 0.7722 (m-10) cc_final: 0.7335 (m-80)
REVERT: D   74 THR cc_start: 0.8039 (t) cc_final: 0.7762 (p)
REVERT: D   75 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7789 (t)
REVERT: D  126 SER cc_start: 0.8663 (t) cc_final: 0.8426 (m)
REVERT: D  213 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: D  329 ILE cc_start: 0.8431 (tp) cc_final: 0.8223 (tt)
REVERT: D  336 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7905 (ttt180)
REVERT: H   30 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.8211 (t)
REVERT: H   63 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8251 (t)
  outliers start: 42
  outliers final: 25
  residues processed: 265
  average time/residue: 0.5176
  time to fit residues: 146.7754
Evaluate side-chains
  268 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 238
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  346 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 13 optimal weight:    0.0570
   chunk 15 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 110 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 96 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
D 304 ASN
H 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.130798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.116740 restraints weight = 12162.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.92
r_work: 0.3360 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9200  Z= 0.146
  Angle     :  0.597  10.375  12492  Z= 0.301
  Chirality :  0.043   0.189   1437
  Planarity :  0.004   0.037   1576
  Dihedral  :  5.180  70.200   1262
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 23.17 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.25), residues: 1150
  helix:  1.95 (0.25), residues: 410
  sheet: -0.28 (0.29), residues: 294
  loop : -0.06 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.016   0.001   TYR D 179 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B 339 
 HIS   0.003   0.001   HIS D 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9196)
  covalent geometry    : angle       0.59544 (12484)
  SS BOND              : bond        0.00622 (    4)
  SS BOND              : angle       1.63422 (    8)
  hydrogen bonds       : bond        0.03667 (  482)
  hydrogen bonds       : angle       4.64898 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 240
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8522 (p) cc_final: 0.8231 (p)
REVERT: A    9 ASP cc_start: 0.7889 (m-30) cc_final: 0.7629 (m-30)
REVERT: A   10 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8156 (mtmm)
REVERT: A   39 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7152 (mt-10)
REVERT: A  290 ASP cc_start: 0.7713 (m-30) cc_final: 0.7386 (m-30)
REVERT: A  307 GLU cc_start: 0.7994 (tp30) cc_final: 0.7668 (tp30)
REVERT: A  322 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7794 (ttmm)
REVERT: B   37 ILE cc_start: 0.7965 (mm) cc_final: 0.7641 (tt)
REVERT: B   52 ARG cc_start: 0.7711 (ttm110) cc_final: 0.7370 (mtp85)
REVERT: B   87 THR cc_start: 0.7979 (m) cc_final: 0.7699 (t)
REVERT: B   98 SER cc_start: 0.8108 (p) cc_final: 0.7732 (t)
REVERT: B  161 SER cc_start: 0.7856 (p) cc_final: 0.7648 (m)
REVERT: B  170 ASP cc_start: 0.7932 (t70) cc_final: 0.7507 (t0)
REVERT: B  212 ASP cc_start: 0.7706 (t70) cc_final: 0.7460 (t0)
REVERT: B  221 THR cc_start: 0.8279 (t) cc_final: 0.8063 (m)
REVERT: B  227 SER cc_start: 0.8591 (m) cc_final: 0.8109 (t)
REVERT: B  271 CYS cc_start: 0.8037 (m) cc_final: 0.7752 (p)
REVERT: B  289 TYR cc_start: 0.7642 (m-10) cc_final: 0.7236 (m-80)
REVERT: D   74 THR cc_start: 0.7955 (t) cc_final: 0.7668 (p)
REVERT: D   75 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7761 (t)
REVERT: D  126 SER cc_start: 0.8642 (t) cc_final: 0.8435 (m)
REVERT: D  329 ILE cc_start: 0.8434 (tp) cc_final: 0.8223 (tt)
REVERT: D  336 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7869 (ttt180)
REVERT: G   38 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7482 (ttp)
REVERT: H   30 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.8219 (t)
REVERT: H   63 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8182 (t)
  outliers start: 34
  outliers final: 25
  residues processed: 257
  average time/residue: 0.5407
  time to fit residues: 148.3751
Evaluate side-chains
  269 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 239
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0670
   chunk 82 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.130376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.116163 restraints weight = 12159.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.92
r_work: 0.3342 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9200  Z= 0.146
  Angle     :  0.604  11.611  12492  Z= 0.305
  Chirality :  0.044   0.197   1437
  Planarity :  0.004   0.037   1576
  Dihedral  :  5.147  70.285   1262
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 23.49 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.25), residues: 1150
  helix:  1.91 (0.26), residues: 410
  sheet: -0.23 (0.30), residues: 287
  loop : -0.17 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  38 
 TYR   0.022   0.001   TYR D 237 
 PHE   0.014   0.002   PHE B 199 
 TRP   0.014   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9196)
  covalent geometry    : angle       0.60234 (12484)
  SS BOND              : bond        0.00671 (    4)
  SS BOND              : angle       1.68032 (    8)
  hydrogen bonds       : bond        0.03680 (  482)
  hydrogen bonds       : angle       4.67041 ( 1335)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 241
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7865 (m-30) cc_final: 0.7651 (m-30)
REVERT: A   10 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8149 (mtmm)
REVERT: A   57 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7593 (mtpt)
REVERT: A  201 PHE cc_start: 0.8548 (m-80) cc_final: 0.7669 (m-80)
REVERT: A  290 ASP cc_start: 0.7726 (m-30) cc_final: 0.7405 (m-30)
REVERT: A  307 GLU cc_start: 0.8028 (tp30) cc_final: 0.7689 (tp30)
REVERT: A  322 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7864 (ttmm)
REVERT: B   37 ILE cc_start: 0.7981 (mm) cc_final: 0.7640 (tt)
REVERT: B   52 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7384 (mtp85)
REVERT: B   87 THR cc_start: 0.7906 (m) cc_final: 0.7644 (t)
REVERT: B   98 SER cc_start: 0.8117 (p) cc_final: 0.7755 (t)
REVERT: B  161 SER cc_start: 0.7874 (p) cc_final: 0.7648 (m)
REVERT: B  170 ASP cc_start: 0.7937 (t70) cc_final: 0.7527 (t0)
REVERT: B  212 ASP cc_start: 0.7701 (t70) cc_final: 0.7453 (t0)
REVERT: B  221 THR cc_start: 0.8275 (t) cc_final: 0.8056 (m)
REVERT: B  227 SER cc_start: 0.8587 (m) cc_final: 0.8048 (t)
REVERT: B  230 ASN cc_start: 0.8446 (m-40) cc_final: 0.8038 (m110)
REVERT: B  246 ASP cc_start: 0.7711 (m-30) cc_final: 0.7419 (m-30)
REVERT: B  258 ASP cc_start: 0.7400 (m-30) cc_final: 0.7186 (m-30)
REVERT: B  271 CYS cc_start: 0.8048 (m) cc_final: 0.7752 (p)
REVERT: B  289 TYR cc_start: 0.7649 (m-10) cc_final: 0.7314 (m-80)
REVERT: D   44 GLN cc_start: 0.8170 (tt0) cc_final: 0.7954 (tp40)
REVERT: D   74 THR cc_start: 0.7991 (t) cc_final: 0.7710 (p)
REVERT: D   75 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7743 (t)
REVERT: D  115 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7705 (mmpt)
REVERT: D  126 SER cc_start: 0.8648 (t) cc_final: 0.8427 (m)
REVERT: D  329 ILE cc_start: 0.8439 (tp) cc_final: 0.8229 (tt)
REVERT: D  336 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7884 (ttt180)
REVERT: H   30 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8238 (t)
REVERT: H   67 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7950 (ttp80)
  outliers start: 32
  outliers final: 22
  residues processed: 256
  average time/residue: 0.5540
  time to fit residues: 151.4679
Evaluate side-chains
  265 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 240
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0980
   chunk 10 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.131275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.117107 restraints weight = 12020.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.91
r_work: 0.3365 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9200  Z= 0.142
  Angle     :  0.613  10.951  12492  Z= 0.308
  Chirality :  0.044   0.210   1437
  Planarity :  0.004   0.037   1576
  Dihedral  :  5.110  69.962   1262
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 23.80 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1150
  helix:  1.92 (0.26), residues: 410
  sheet: -0.28 (0.30), residues: 289
  loop : -0.20 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.024   0.001   TYR D 237 
 PHE   0.014   0.002   PHE B 199 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS D 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9196)
  covalent geometry    : angle       0.61197 (12484)
  SS BOND              : bond        0.00667 (    4)
  SS BOND              : angle       1.71024 (    8)
  hydrogen bonds       : bond        0.03647 (  482)
  hydrogen bonds       : angle       4.67264 ( 1335)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3819.24 seconds
wall clock time: 65 minutes 43.27 seconds (3943.27 seconds total)