Starting phenix.real_space_refine
on Wed Sep 17 10:11:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lyb_63525/09_2025/9lyb_63525_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lyb_63525/09_2025/9lyb_63525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lyb_63525/09_2025/9lyb_63525_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lyb_63525/09_2025/9lyb_63525_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lyb_63525/09_2025/9lyb_63525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lyb_63525/09_2025/9lyb_63525.map"
  }
  resolution = 3.16
  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=   0.001 sd=   0.022
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      57      5.16       5
     C    5073      2.51       5
     N    1392      2.21       5
     O    1481      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8003
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1958
          Classifications: {'peptide': 240}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2589
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 431
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "N"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "R"
      Number of atoms: 2054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2054
          Classifications: {'peptide': 272}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 260}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   SER N 127 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  SER N 127 " occ=0.50
  Time building chain proxies: 2.16, per 1000 atoms: 0.27
  Number of scatterers: 8003
  At special positions: 0
  Unit cell: (75.92, 98.8, 130, 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      57     16.00
     O    1481      8.00
     N    1392      7.00
     C    5073      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 177 " - pdb=" SG  CYS R 184 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 498.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      42.7% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 40
      removed outlier: 3.617A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.629A  pdb=" N   LEU A  63 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.590A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.864A  pdb=" N   LYS A 271 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ILE A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.117A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 4.179A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.855A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.634A  pdb=" N   ILE A 383 " --> pdb=" O   CYS A 379 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLN A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   HIS A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 4.053A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.802A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.631A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 42 through 68
      removed outlier: 3.753A  pdb=" N   ILE R  49 " --> pdb=" O   VAL R  45 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   SER R  50 " --> pdb=" O   VAL R  46 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ALA R  59 " --> pdb=" O   SER R  55 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   VAL R  61 " --> pdb=" O   GLU R  57 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE R  65 " --> pdb=" O   VAL R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 103
    Processing helix  chain 'R' and resid 105 through 140
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 4.527A  pdb=" N   TYR R 145 " --> pdb=" O   ALA R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 150
    Processing helix  chain 'R' and resid 152 through 168
      removed outlier: 4.376A  pdb=" N   GLY R 166 " --> pdb=" O   GLY R 162 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU R 167 " --> pdb=" O   GLY R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 169 through 174
      removed outlier: 3.731A  pdb=" N   ALA R 174 " --> pdb=" O   LEU R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 231
      removed outlier: 3.562A  pdb=" N   LEU R 195 " --> pdb=" O   SER R 191 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL R 197 " --> pdb=" O   ASN R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 243 through 270
      removed outlier: 4.209A  pdb=" N   PHE R 256 " --> pdb=" O   VAL R 252 " (cutoff:3.500A)
      Proline residue:  R 262  - end of helix
    Processing helix  chain 'R' and resid 275 through 298
      removed outlier: 3.894A  pdb=" N   THR R 279 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      Proline residue:  R 285  - end of helix
      removed outlier: 4.125A  pdb=" N   SER R 290 " --> pdb=" O   ALA R 286 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   MET R 291 " --> pdb=" O   THR R 287 " (cutoff:3.500A)
      Proline residue:  R 294  - end of helix
    Processing helix  chain 'R' and resid 301 through 314
      removed outlier: 3.512A  pdb=" N   ALA R 310 " --> pdb=" O   LYS R 306 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   CYS R 313 " --> pdb=" O   TRP R 309 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 4.188A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.274A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.647A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.394A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.854A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.316A  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: 3.587A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.610A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.760A  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: 3.663A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.925A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    427 hydrogen bonds defined for protein.
    1221 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: 1.21

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2631
        1.34 -     1.46: 1811
        1.46 -     1.58: 3640
        1.58 -     1.70: 0
        1.70 -     1.81: 78
  Bond restraints: 8160
  Sorted by residual:
  bond pdb=" N   LEU R 142 "
       pdb=" CA  LEU R 142 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.021 1.23e-02 6.61e+03 2.97e+00
  bond pdb=" N   ASN R 140 "
       pdb=" CA  ASN R 140 "
    ideal  model  delta    sigma   weight residual
    1.462  1.486 -0.024 1.44e-02 4.82e+03 2.73e+00
  bond pdb=" CA  ALA R 141 "
       pdb=" CB  ALA R 141 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.55e-02 4.16e+03 2.51e+00
  bond pdb=" N   ALA R 141 "
       pdb=" CA  ALA R 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.475 -0.016 1.19e-02 7.06e+03 1.82e+00
  bond pdb=" CB  ILE R 216 "
       pdb=" CG2 ILE R 216 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  ... (remaining 8155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 10874
        1.92 -     3.85: 164
        3.85 -     5.77: 29
        5.77 -     7.69: 3
        7.69 -     9.62: 5
  Bond angle restraints: 11075
  Sorted by residual:
  angle pdb=" N   VAL R 150 "
        pdb=" CA  VAL R 150 "
        pdb=" C   VAL R 150 "
      ideal   model   delta    sigma   weight residual
     112.96  106.90    6.06 1.00e+00 1.00e+00 3.67e+01
  angle pdb=" N   VAL R 186 "
        pdb=" CA  VAL R 186 "
        pdb=" C   VAL R 186 "
      ideal   model   delta    sigma   weight residual
     113.43  108.17    5.26 1.09e+00 8.42e-01 2.33e+01
  angle pdb=" CA  MET R 209 "
        pdb=" CB  MET R 209 "
        pdb=" CG  MET R 209 "
      ideal   model   delta    sigma   weight residual
     114.10  122.78   -8.68 2.00e+00 2.50e-01 1.89e+01
  angle pdb=" C   TYR R 188 "
        pdb=" N   PRO R 189 "
        pdb=" CD  PRO R 189 "
      ideal   model   delta    sigma   weight residual
     120.60  112.51    8.09 2.20e+00 2.07e-01 1.35e+01
  angle pdb=" CA  ASN R 140 "
        pdb=" C   ASN R 140 "
        pdb=" O   ASN R 140 "
      ideal   model   delta    sigma   weight residual
     122.51  118.07    4.44 1.34e+00 5.57e-01 1.10e+01
  ... (remaining 11070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 4440
       16.40 -    32.79: 323
       32.79 -    49.19: 77
       49.19 -    65.58: 11
       65.58 -    81.98: 6
  Dihedral angle restraints: 4857
    sinusoidal: 1852
      harmonic: 3005
  Sorted by residual:
  dihedral pdb=" CB  CYS R 177 "
           pdb=" SG  CYS R 177 "
           pdb=" SG  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.64   72.64     1      1.00e+01 1.00e-02 6.74e+01
  dihedral pdb=" CA  ALA R  42 "
           pdb=" C   ALA R  42 "
           pdb=" N   TRP R  43 "
           pdb=" CA  TRP R  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.28  -19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 4854 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 881
       0.037 -    0.073: 282
       0.073 -    0.110: 90
       0.110 -    0.147: 19
       0.147 -    0.184: 3
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  ASN R 140 "
            pdb=" N   ASN R 140 "
            pdb=" C   ASN R 140 "
            pdb=" CB  ASN R 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.42e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.99e-01
  ... (remaining 1272 not shown)

  Planarity restraints: 1411
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 188 "   -0.054 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO R 189 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO R 189 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO R 189 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 139 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.31e+00
        pdb=" C   TYR R 139 "    0.050 2.00e-02 2.50e+03
        pdb=" O   TYR R 139 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN R 140 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.021 2.00e-02 2.50e+03   1.47e-02 4.35e+00
        pdb=" CG  TYR B  59 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1408 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 115
        2.67 -     3.23: 7531
        3.23 -     3.78: 12342
        3.78 -     4.34: 16719
        4.34 -     4.90: 27538
  Nonbonded interactions: 64245
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" O   ALA R 106 "
            pdb=" OG  SER R 109 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   TYR R 144 "
            pdb=" OG1 THR R 149 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.261 3.040
  ... (remaining 64240 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=0.00 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.190
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
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      :  0.003   0.043   8163  Z= 0.138
  Angle     :  0.605   9.616  11081  Z= 0.334
  Chirality :  0.041   0.184   1275
  Planarity :  0.005   0.083   1411
  Dihedral  : 12.555  81.976   2908
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  0.50 (0.26), residues: 1021
  helix:  1.10 (0.26), residues: 396
  sheet:  0.73 (0.34), residues: 224
  loop : -0.60 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG N 118 
 TYR   0.035   0.001   TYR B  59 
 PHE   0.016   0.001   PHE B 234 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8160)
  covalent geometry    : angle       0.60474 (11075)
  SS BOND              : bond        0.00130 (    3)
  SS BOND              : angle       0.68955 (    6)
  hydrogen bonds       : bond        0.17762 (  427)
  hydrogen bonds       : angle       6.28508 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 LYS cc_start: 0.8200 (mttm) cc_final: 0.7958 (mttm)
REVERT: A  223 ASP cc_start: 0.6549 (t0) cc_final: 0.6333 (t0)
REVERT: A  231 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7711 (ptp-170)
REVERT: A  278 ASN cc_start: 0.7744 (m-40) cc_final: 0.7415 (m110)
REVERT: A  292 ASN cc_start: 0.8154 (t0) cc_final: 0.7945 (t0)
REVERT: A  386 MET cc_start: 0.7769 (tmm) cc_final: 0.7511 (tmm)
REVERT: B   46 ARG cc_start: 0.6938 (mtm180) cc_final: 0.6644 (mtm180)
REVERT: B   98 SER cc_start: 0.7996 (m) cc_final: 0.7670 (t)
REVERT: B  120 ILE cc_start: 0.7246 (mt) cc_final: 0.7028 (mm)
REVERT: B  125 ASN cc_start: 0.8065 (t0) cc_final: 0.7748 (t0)
REVERT: B  137 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7255 (tpp-160)
REVERT: B  155 ASN cc_start: 0.7803 (t0) cc_final: 0.7386 (t0)
REVERT: B  198 LEU cc_start: 0.8593 (mt) cc_final: 0.8351 (mp)
REVERT: B  219 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6350 (mmm160)
REVERT: B  230 ASN cc_start: 0.8270 (m-40) cc_final: 0.7858 (m110)
REVERT: B  239 ASN cc_start: 0.7516 (m110) cc_final: 0.6766 (m-40)
REVERT: B  254 ASP cc_start: 0.6764 (t70) cc_final: 0.6064 (t70)
REVERT: B  256 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7067 (mtm180)
REVERT: B  258 ASP cc_start: 0.7001 (t70) cc_final: 0.6759 (t0)
REVERT: B  277 SER cc_start: 0.8054 (p) cc_final: 0.7618 (m)
REVERT: B  295 ASN cc_start: 0.8190 (m-40) cc_final: 0.7928 (m-40)
REVERT: N   46 GLU cc_start: 0.7058 (tt0) cc_final: 0.6843 (tt0)
REVERT: N   50 ASP cc_start: 0.6705 (p0) cc_final: 0.6350 (p0)
REVERT: N  120 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7387 (mm-40)
REVERT: R  108 MET cc_start: 0.4450 (tpp) cc_final: 0.3887 (tpp)
REVERT: R  120 PHE cc_start: 0.8182 (m-10) cc_final: 0.7847 (m-10)
REVERT: R  143 THR cc_start: 0.8242 (m) cc_final: 0.7898 (p)
REVERT: R  188 TYR cc_start: 0.7251 (t80) cc_final: 0.7000 (t80)
REVERT: R  208 ILE cc_start: 0.7936 (mt) cc_final: 0.7698 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1303
  time to fit residues: 42.0897
Evaluate side-chains
  229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  53 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.137880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.121423 restraints weight = 11665.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.03
r_work: 0.3368 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8163  Z= 0.181
  Angle     :  0.599   7.400  11081  Z= 0.316
  Chirality :  0.043   0.230   1275
  Planarity :  0.004   0.052   1411
  Dihedral  :  4.436  20.063   1123
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.51 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1021
  helix:  1.62 (0.26), residues: 399
  sheet:  0.81 (0.34), residues: 220
  loop : -0.40 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  68 
 TYR   0.026   0.002   TYR B  59 
 PHE   0.014   0.002   PHE R  97 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8160)
  covalent geometry    : angle       0.59856 (11075)
  SS BOND              : bond        0.01202 (    3)
  SS BOND              : angle       1.35830 (    6)
  hydrogen bonds       : bond        0.04194 (  427)
  hydrogen bonds       : angle       4.67527 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 215
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.7993 (p) cc_final: 0.7652 (m)
REVERT: A  300 LYS cc_start: 0.7497 (mtpt) cc_final: 0.7194 (mtpt)
REVERT: A  343 ASP cc_start: 0.8252 (m-30) cc_final: 0.7972 (m-30)
REVERT: A  356 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7875 (mtp180)
REVERT: B   18 ILE cc_start: 0.8727 (mm) cc_final: 0.8508 (mm)
REVERT: B   49 ARG cc_start: 0.8618 (mmt90) cc_final: 0.8346 (mpt180)
REVERT: B   98 SER cc_start: 0.8642 (m) cc_final: 0.8325 (t)
REVERT: B  137 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7772 (tpp-160)
REVERT: B  212 ASP cc_start: 0.7587 (m-30) cc_final: 0.6921 (m-30)
REVERT: B  219 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7203 (ttm-80)
REVERT: B  230 ASN cc_start: 0.8501 (m-40) cc_final: 0.8101 (m110)
REVERT: B  258 ASP cc_start: 0.8059 (t70) cc_final: 0.7393 (t0)
REVERT: B  268 ASN cc_start: 0.8307 (m-40) cc_final: 0.7813 (t0)
REVERT: B  277 SER cc_start: 0.8259 (p) cc_final: 0.7813 (m)
REVERT: B  289 TYR cc_start: 0.8578 (m-80) cc_final: 0.8168 (m-80)
REVERT: N    7 SER cc_start: 0.8299 (p) cc_final: 0.8057 (t)
REVERT: N   86 LEU cc_start: 0.8695 (mt) cc_final: 0.8484 (mt)
REVERT: N  120 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8241 (mm-40)
REVERT: R   53 LEU cc_start: 0.7341 (mt) cc_final: 0.7078 (mt)
REVERT: R  209 MET cc_start: 0.8471 (tpp) cc_final: 0.8208 (mmt)
  outliers start: 15
  outliers final: 8
  residues processed: 219
  average time/residue: 0.1325
  time to fit residues: 36.2165
Evaluate side-chains
  214 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 206
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  118 MET
Chi-restraints excluded: chain R residue  273 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
R  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.115734 restraints weight = 11408.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.03
r_work: 0.3320 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3108
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3108
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8163  Z= 0.204
  Angle     :  0.585   8.872  11081  Z= 0.308
  Chirality :  0.042   0.155   1275
  Planarity :  0.004   0.033   1411
  Dihedral  :  4.509  20.585   1123
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 12.68 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  0.93 (0.26), residues: 1021
  helix:  1.61 (0.26), residues: 405
  sheet:  0.60 (0.35), residues: 219
  loop : -0.33 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 300 
 TYR   0.017   0.002   TYR B  59 
 PHE   0.015   0.002   PHE A 212 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8160)
  covalent geometry    : angle       0.58464 (11075)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       0.91389 (    6)
  hydrogen bonds       : bond        0.04494 (  427)
  hydrogen bonds       : angle       4.66218 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 223
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8276 (mtpp) cc_final: 0.8022 (mtpp)
REVERT: A  242 THR cc_start: 0.8863 (p) cc_final: 0.8548 (m)
REVERT: A  271 LYS cc_start: 0.8327 (mmtp) cc_final: 0.8112 (mmmm)
REVERT: A  292 ASN cc_start: 0.8746 (t0) cc_final: 0.8531 (t0)
REVERT: A  300 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7269 (mtpt)
REVERT: A  343 ASP cc_start: 0.8168 (m-30) cc_final: 0.7935 (m-30)
REVERT: A  372 ILE cc_start: 0.8156 (pt) cc_final: 0.7898 (mm)
REVERT: A  392 GLU cc_start: 0.7501 (pt0) cc_final: 0.7289 (pt0)
REVERT: B    6 GLN cc_start: 0.7008 (pp30) cc_final: 0.6723 (pp30)
REVERT: B   13 GLN cc_start: 0.7815 (pp30) cc_final: 0.7535 (pp30)
REVERT: B   18 ILE cc_start: 0.8760 (mm) cc_final: 0.8543 (mm)
REVERT: B   22 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8380 (mtm-85)
REVERT: B   38 ASP cc_start: 0.8209 (m-30) cc_final: 0.8001 (m-30)
REVERT: B   46 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7846 (mtm180)
REVERT: B   49 ARG cc_start: 0.8671 (mmt90) cc_final: 0.8361 (mpt90)
REVERT: B   61 MET cc_start: 0.8424 (ppp) cc_final: 0.7666 (ppp)
REVERT: B   75 GLN cc_start: 0.8340 (mm110) cc_final: 0.7927 (mm110)
REVERT: B   98 SER cc_start: 0.8729 (m) cc_final: 0.8257 (t)
REVERT: B  137 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7774 (tpp-160)
REVERT: B  198 LEU cc_start: 0.8931 (mt) cc_final: 0.8701 (mp)
REVERT: B  230 ASN cc_start: 0.8486 (m-40) cc_final: 0.8104 (m-40)
REVERT: B  234 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8475 (m-80)
REVERT: B  258 ASP cc_start: 0.8110 (t70) cc_final: 0.7225 (t70)
REVERT: B  277 SER cc_start: 0.8332 (p) cc_final: 0.7878 (m)
REVERT: G   20 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8079 (mtmm)
REVERT: G   27 ARG cc_start: 0.8717 (mtt-85) cc_final: 0.8128 (mtt-85)
REVERT: R   53 LEU cc_start: 0.7518 (mt) cc_final: 0.7272 (mt)
REVERT: R   61 VAL cc_start: 0.8467 (p) cc_final: 0.8207 (t)
REVERT: R  137 SER cc_start: 0.8798 (t) cc_final: 0.8523 (p)
REVERT: R  209 MET cc_start: 0.8415 (tpp) cc_final: 0.8185 (mmt)
REVERT: R  249 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7958 (tt)
  outliers start: 18
  outliers final: 10
  residues processed: 230
  average time/residue: 0.1443
  time to fit residues: 40.8818
Evaluate side-chains
  226 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 214
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  273 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.130610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.114077 restraints weight = 11779.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.11
r_work: 0.3269 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8163  Z= 0.180
  Angle     :  0.549   9.540  11081  Z= 0.289
  Chirality :  0.041   0.133   1275
  Planarity :  0.004   0.042   1411
  Dihedral  :  4.404  18.466   1123
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.20 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.07 (0.27), residues: 1021
  helix:  1.77 (0.26), residues: 406
  sheet:  0.44 (0.35), residues: 219
  loop : -0.16 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  68 
 TYR   0.016   0.001   TYR B  59 
 PHE   0.012   0.002   PHE N 108 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8160)
  covalent geometry    : angle       0.54792 (11075)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       1.80436 (    6)
  hydrogen bonds       : bond        0.04116 (  427)
  hydrogen bonds       : angle       4.54047 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 228
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6921 (mm-30)
REVERT: A  211 LYS cc_start: 0.8299 (mtpp) cc_final: 0.8069 (mtpp)
REVERT: A  274 ASP cc_start: 0.8172 (t0) cc_final: 0.7875 (t0)
REVERT: A  283 ARG cc_start: 0.7913 (mmt180) cc_final: 0.7712 (mmt180)
REVERT: A  292 ASN cc_start: 0.8677 (t0) cc_final: 0.8393 (t0)
REVERT: A  300 LYS cc_start: 0.7562 (mtpt) cc_final: 0.7290 (mtpt)
REVERT: B    6 GLN cc_start: 0.7185 (pp30) cc_final: 0.6859 (pp30)
REVERT: B   13 GLN cc_start: 0.7819 (pp30) cc_final: 0.7534 (pp30)
REVERT: B   18 ILE cc_start: 0.8720 (mm) cc_final: 0.8476 (mm)
REVERT: B   49 ARG cc_start: 0.8654 (mmt90) cc_final: 0.8376 (mpt180)
REVERT: B   61 MET cc_start: 0.8371 (ppp) cc_final: 0.7719 (ppp)
REVERT: B   98 SER cc_start: 0.8676 (m) cc_final: 0.8316 (p)
REVERT: B  214 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7471 (mtm110)
REVERT: B  234 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8424 (m-80)
REVERT: B  258 ASP cc_start: 0.8154 (t70) cc_final: 0.7477 (t70)
REVERT: B  277 SER cc_start: 0.8292 (p) cc_final: 0.7805 (m)
REVERT: B  289 TYR cc_start: 0.8680 (m-80) cc_final: 0.8262 (m-80)
REVERT: G   20 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7972 (mtmm)
REVERT: R   61 VAL cc_start: 0.8462 (p) cc_final: 0.8197 (t)
REVERT: R   72 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7505 (mmm-85)
REVERT: R   82 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8641 (tp)
REVERT: R  209 MET cc_start: 0.8466 (tpp) cc_final: 0.7930 (mmm)
REVERT: R  249 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7921 (tt)
REVERT: R  291 MET cc_start: 0.8106 (mmp) cc_final: 0.7837 (mmp)
  outliers start: 25
  outliers final: 14
  residues processed: 237
  average time/residue: 0.1436
  time to fit residues: 41.8647
Evaluate side-chains
  238 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 220
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  118 MET
Chi-restraints excluded: chain R residue  186 VAL
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  273 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0870
   chunk 93 optimal weight:    0.0370
   chunk 36 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0980
   chunk 60 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.2836

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.132790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.116308 restraints weight = 11716.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.10
r_work: 0.3305 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8163  Z= 0.106
  Angle     :  0.494   9.713  11081  Z= 0.258
  Chirality :  0.039   0.136   1275
  Planarity :  0.003   0.033   1411
  Dihedral  :  4.094  20.001   1123
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.31 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.23 (0.27), residues: 1021
  helix:  2.03 (0.26), residues: 406
  sheet:  0.40 (0.34), residues: 219
  loop : -0.14 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  68 
 TYR   0.012   0.001   TYR R 297 
 PHE   0.010   0.001   PHE A 222 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8160)
  covalent geometry    : angle       0.49404 (11075)
  SS BOND              : bond        0.00161 (    3)
  SS BOND              : angle       0.70764 (    6)
  hydrogen bonds       : bond        0.03564 (  427)
  hydrogen bonds       : angle       4.28409 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 222
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6844 (mm-30)
REVERT: A  211 LYS cc_start: 0.8281 (mtpp) cc_final: 0.8049 (mtpp)
REVERT: A  242 THR cc_start: 0.8813 (p) cc_final: 0.8534 (m)
REVERT: A  292 ASN cc_start: 0.8614 (t0) cc_final: 0.8286 (t0)
REVERT: A  300 LYS cc_start: 0.7558 (mtpt) cc_final: 0.7211 (mtpt)
REVERT: A  381 ASP cc_start: 0.7816 (t0) cc_final: 0.7579 (t0)
REVERT: B   13 GLN cc_start: 0.7852 (pp30) cc_final: 0.7583 (pp30)
REVERT: B   59 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7991 (t80)
REVERT: B   61 MET cc_start: 0.8308 (ppp) cc_final: 0.7816 (ppp)
REVERT: B   75 GLN cc_start: 0.8119 (mm110) cc_final: 0.7855 (mm110)
REVERT: B   98 SER cc_start: 0.8555 (m) cc_final: 0.8216 (p)
REVERT: B  230 ASN cc_start: 0.8395 (m-40) cc_final: 0.8003 (m-40)
REVERT: B  234 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8273 (m-80)
REVERT: B  258 ASP cc_start: 0.8141 (t70) cc_final: 0.7336 (t70)
REVERT: B  277 SER cc_start: 0.8315 (p) cc_final: 0.7789 (m)
REVERT: B  289 TYR cc_start: 0.8649 (m-80) cc_final: 0.8201 (m-80)
REVERT: N  120 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8223 (mm-40)
REVERT: R   61 VAL cc_start: 0.8335 (p) cc_final: 0.8064 (t)
REVERT: R   72 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7410 (mmm-85)
REVERT: R   82 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8587 (tp)
REVERT: R  120 PHE cc_start: 0.8662 (m-10) cc_final: 0.8457 (m-10)
REVERT: R  137 SER cc_start: 0.8890 (t) cc_final: 0.8640 (p)
REVERT: R  209 MET cc_start: 0.8456 (tpp) cc_final: 0.7952 (mmm)
REVERT: R  249 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7787 (tt)
REVERT: R  291 MET cc_start: 0.8171 (mmp) cc_final: 0.7913 (mmp)
  outliers start: 20
  outliers final: 8
  residues processed: 228
  average time/residue: 0.1427
  time to fit residues: 40.0667
Evaluate side-chains
  223 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 211
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.129848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.112958 restraints weight = 11565.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.09
r_work: 0.3263 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8163  Z= 0.191
  Angle     :  0.567  10.055  11081  Z= 0.295
  Chirality :  0.042   0.141   1275
  Planarity :  0.004   0.039   1411
  Dihedral  :  4.295  18.651   1123
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.25 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.37 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.17 (0.27), residues: 1021
  helix:  1.97 (0.26), residues: 407
  sheet:  0.32 (0.34), residues: 215
  loop : -0.13 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 231 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.014   0.002   PHE A 212 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8160)
  covalent geometry    : angle       0.56724 (11075)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       0.84297 (    6)
  hydrogen bonds       : bond        0.04174 (  427)
  hydrogen bonds       : angle       4.50040 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 211
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6898 (mm-30)
REVERT: A  211 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8067 (mtpp)
REVERT: A  242 THR cc_start: 0.8838 (p) cc_final: 0.8597 (m)
REVERT: A  274 ASP cc_start: 0.8119 (t0) cc_final: 0.7905 (t0)
REVERT: A  292 ASN cc_start: 0.8649 (t0) cc_final: 0.8305 (t0)
REVERT: A  300 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7236 (mtpt)
REVERT: B    6 GLN cc_start: 0.7222 (pp30) cc_final: 0.6845 (pp30)
REVERT: B   13 GLN cc_start: 0.7887 (pp30) cc_final: 0.7588 (pp30)
REVERT: B   59 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.8033 (t80)
REVERT: B   61 MET cc_start: 0.8330 (ppp) cc_final: 0.7824 (ppp)
REVERT: B   87 THR cc_start: 0.8425 (m) cc_final: 0.8138 (t)
REVERT: B   98 SER cc_start: 0.8620 (m) cc_final: 0.8310 (p)
REVERT: B  101 MET cc_start: 0.8142 (mtp) cc_final: 0.7754 (mtp)
REVERT: B  234 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8438 (m-80)
REVERT: B  258 ASP cc_start: 0.8152 (t70) cc_final: 0.7283 (t0)
REVERT: B  277 SER cc_start: 0.8315 (p) cc_final: 0.7806 (m)
REVERT: B  289 TYR cc_start: 0.8689 (m-80) cc_final: 0.8215 (m-80)
REVERT: G   20 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8156 (mtmt)
REVERT: G   27 ARG cc_start: 0.8730 (mtt-85) cc_final: 0.8251 (mtt-85)
REVERT: N   34 MET cc_start: 0.8383 (mmm) cc_final: 0.8138 (mmt)
REVERT: R   61 VAL cc_start: 0.8434 (p) cc_final: 0.8175 (t)
REVERT: R   72 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.7622 (mmm-85)
REVERT: R   82 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8640 (tp)
REVERT: R  118 MET cc_start: 0.8404 (ttm) cc_final: 0.8165 (ttm)
REVERT: R  209 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7978 (mtp)
REVERT: R  249 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7894 (tt)
  outliers start: 23
  outliers final: 11
  residues processed: 222
  average time/residue: 0.1441
  time to fit residues: 39.3119
Evaluate side-chains
  224 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 208
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  273 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 73 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.113648 restraints weight = 11622.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.06
r_work: 0.3270 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8163  Z= 0.164
  Angle     :  0.545  10.734  11081  Z= 0.282
  Chirality :  0.041   0.132   1275
  Planarity :  0.004   0.035   1411
  Dihedral  :  4.212  19.251   1123
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.45 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.61 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.24 (0.27), residues: 1021
  helix:  2.04 (0.25), residues: 408
  sheet:  0.34 (0.35), residues: 210
  loop : -0.10 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 231 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.011   0.002   PHE N 108 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8160)
  covalent geometry    : angle       0.54532 (11075)
  SS BOND              : bond        0.00229 (    3)
  SS BOND              : angle       0.59198 (    6)
  hydrogen bonds       : bond        0.03999 (  427)
  hydrogen bonds       : angle       4.43356 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 217
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6874 (mm-30)
REVERT: A  211 LYS cc_start: 0.8302 (mtpp) cc_final: 0.8035 (mtpp)
REVERT: A  242 THR cc_start: 0.8824 (p) cc_final: 0.8606 (m)
REVERT: A  248 VAL cc_start: 0.8383 (t) cc_final: 0.8169 (m)
REVERT: A  274 ASP cc_start: 0.8118 (t0) cc_final: 0.7881 (t0)
REVERT: A  292 ASN cc_start: 0.8637 (t0) cc_final: 0.8296 (t0)
REVERT: A  300 LYS cc_start: 0.7606 (mtpt) cc_final: 0.7273 (mtpt)
REVERT: A  383 ILE cc_start: 0.8685 (pt) cc_final: 0.8205 (mt)
REVERT: B   13 GLN cc_start: 0.7890 (pp30) cc_final: 0.7589 (pp30)
REVERT: B   19 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7737 (ttp-110)
REVERT: B   23 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8340 (ttpt)
REVERT: B   59 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8025 (t80)
REVERT: B   61 MET cc_start: 0.8341 (ppp) cc_final: 0.7901 (ppp)
REVERT: B   87 THR cc_start: 0.8411 (m) cc_final: 0.8103 (t)
REVERT: B   98 SER cc_start: 0.8577 (m) cc_final: 0.8276 (p)
REVERT: B  101 MET cc_start: 0.8106 (mtp) cc_final: 0.7714 (mtp)
REVERT: B  234 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8375 (m-80)
REVERT: B  258 ASP cc_start: 0.8141 (t70) cc_final: 0.7278 (t0)
REVERT: B  277 SER cc_start: 0.8303 (p) cc_final: 0.7803 (m)
REVERT: B  289 TYR cc_start: 0.8722 (m-80) cc_final: 0.8167 (m-80)
REVERT: G   20 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7886 (mtmm)
REVERT: G   27 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8242 (mtt-85)
REVERT: N   34 MET cc_start: 0.8371 (mmm) cc_final: 0.8083 (mmt)
REVERT: N  120 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8255 (mm-40)
REVERT: R   61 VAL cc_start: 0.8397 (p) cc_final: 0.8129 (t)
REVERT: R   72 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7648 (mmm-85)
REVERT: R   82 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8646 (tp)
REVERT: R  118 MET cc_start: 0.8387 (ttm) cc_final: 0.7921 (mtt)
REVERT: R  120 PHE cc_start: 0.8645 (m-10) cc_final: 0.8426 (m-10)
REVERT: R  209 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8046 (mtp)
REVERT: R  249 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7919 (tt)
REVERT: R  291 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8113 (mmt)
  outliers start: 27
  outliers final: 17
  residues processed: 226
  average time/residue: 0.1407
  time to fit residues: 38.8768
Evaluate side-chains
  239 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 215
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  291 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 43 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 83 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 42 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
B  75 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.127181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.111081 restraints weight = 11614.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.99
r_work: 0.3289 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.5033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8163  Z= 0.136
  Angle     :  0.532  10.957  11081  Z= 0.275
  Chirality :  0.040   0.132   1275
  Planarity :  0.004   0.035   1411
  Dihedral  :  4.092  19.395   1123
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.45 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.66 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.28 (0.27), residues: 1021
  helix:  2.12 (0.25), residues: 409
  sheet:  0.27 (0.33), residues: 216
  loop : -0.08 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 231 
 TYR   0.011   0.001   TYR R 297 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8160)
  covalent geometry    : angle       0.53067 (11075)
  SS BOND              : bond        0.00290 (    3)
  SS BOND              : angle       1.78802 (    6)
  hydrogen bonds       : bond        0.03821 (  427)
  hydrogen bonds       : angle       4.35059 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 217
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6861 (mm-30)
REVERT: A  220 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7430 (m90)
REVERT: A  242 THR cc_start: 0.8810 (p) cc_final: 0.8580 (m)
REVERT: A  248 VAL cc_start: 0.8410 (t) cc_final: 0.8201 (m)
REVERT: A  274 ASP cc_start: 0.8123 (t0) cc_final: 0.7871 (t0)
REVERT: A  292 ASN cc_start: 0.8606 (t0) cc_final: 0.8312 (t0)
REVERT: A  300 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7302 (mtpt)
REVERT: B   13 GLN cc_start: 0.7876 (pp30) cc_final: 0.7575 (pp30)
REVERT: B   23 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8328 (ttpt)
REVERT: B   59 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.8026 (t80)
REVERT: B   61 MET cc_start: 0.8297 (ppp) cc_final: 0.7881 (ppp)
REVERT: B   98 SER cc_start: 0.8498 (m) cc_final: 0.8226 (p)
REVERT: B  101 MET cc_start: 0.8049 (mtp) cc_final: 0.7681 (mtp)
REVERT: B  230 ASN cc_start: 0.8413 (m-40) cc_final: 0.8031 (m-40)
REVERT: B  234 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8350 (m-80)
REVERT: B  258 ASP cc_start: 0.8101 (t70) cc_final: 0.7258 (t0)
REVERT: B  277 SER cc_start: 0.8285 (p) cc_final: 0.7793 (m)
REVERT: B  289 TYR cc_start: 0.8713 (m-80) cc_final: 0.8223 (m-80)
REVERT: G   20 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7894 (mtmm)
REVERT: G   27 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8272 (mtt-85)
REVERT: N   86 LEU cc_start: 0.8723 (mt) cc_final: 0.8441 (mt)
REVERT: N  120 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8274 (mm-40)
REVERT: R   61 VAL cc_start: 0.8388 (p) cc_final: 0.8121 (t)
REVERT: R   82 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8657 (tp)
REVERT: R  118 MET cc_start: 0.8300 (ttm) cc_final: 0.7890 (mtt)
REVERT: R  209 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7894 (mtp)
REVERT: R  249 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7945 (tt)
  outliers start: 25
  outliers final: 15
  residues processed: 226
  average time/residue: 0.1408
  time to fit residues: 39.1810
Evaluate side-chains
  236 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 214
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  296 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 82 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
B  75 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.112811 restraints weight = 11538.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.11
r_work: 0.3254 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.5143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8163  Z= 0.189
  Angle     :  0.569  11.011  11081  Z= 0.294
  Chirality :  0.041   0.131   1275
  Planarity :  0.004   0.046   1411
  Dihedral  :  4.285  21.248   1123
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.55 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.90 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.18 (0.27), residues: 1021
  helix:  2.04 (0.26), residues: 405
  sheet:  0.26 (0.34), residues: 210
  loop : -0.15 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG R 231 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.013   0.002   PHE R 120 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8160)
  covalent geometry    : angle       0.56790 (11075)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       1.52802 (    6)
  hydrogen bonds       : bond        0.04175 (  427)
  hydrogen bonds       : angle       4.48546 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 207
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6946 (mm-30)
REVERT: A  274 ASP cc_start: 0.8104 (t0) cc_final: 0.7845 (t0)
REVERT: A  292 ASN cc_start: 0.8642 (t0) cc_final: 0.8376 (t0)
REVERT: A  300 LYS cc_start: 0.7654 (mtpt) cc_final: 0.7331 (mtpt)
REVERT: B   13 GLN cc_start: 0.7881 (pp30) cc_final: 0.7570 (pp30)
REVERT: B   23 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8366 (ttpt)
REVERT: B   49 ARG cc_start: 0.8544 (mpt-90) cc_final: 0.8340 (mpt90)
REVERT: B   59 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.8098 (t80)
REVERT: B   61 MET cc_start: 0.8359 (ppp) cc_final: 0.7909 (ppp)
REVERT: B   87 THR cc_start: 0.8408 (m) cc_final: 0.8067 (t)
REVERT: B   98 SER cc_start: 0.8557 (m) cc_final: 0.8282 (p)
REVERT: B  219 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7353 (mmm160)
REVERT: B  234 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8377 (m-80)
REVERT: B  251 ARG cc_start: 0.8852 (mtt90) cc_final: 0.8547 (ttm170)
REVERT: B  258 ASP cc_start: 0.8164 (t70) cc_final: 0.7280 (t0)
REVERT: B  277 SER cc_start: 0.8327 (p) cc_final: 0.7820 (m)
REVERT: G   20 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7920 (mtmm)
REVERT: G   27 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8238 (mtt-85)
REVERT: N  120 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8250 (mm-40)
REVERT: R   61 VAL cc_start: 0.8398 (p) cc_final: 0.8147 (t)
REVERT: R  118 MET cc_start: 0.8424 (ttm) cc_final: 0.7879 (mtt)
REVERT: R  209 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7959 (mtp)
REVERT: R  249 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7948 (tt)
REVERT: R  291 MET cc_start: 0.8164 (mmt) cc_final: 0.7895 (mmp)
  outliers start: 25
  outliers final: 15
  residues processed: 217
  average time/residue: 0.1432
  time to fit residues: 38.3147
Evaluate side-chains
  228 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  296 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.114763 restraints weight = 11452.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.09
r_work: 0.3273 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.5179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8163  Z= 0.136
  Angle     :  0.538  11.169  11081  Z= 0.277
  Chirality :  0.040   0.131   1275
  Planarity :  0.004   0.041   1411
  Dihedral  :  4.151  20.830   1123
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.35 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.95 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.25 (0.27), residues: 1021
  helix:  2.19 (0.25), residues: 404
  sheet:  0.15 (0.33), residues: 224
  loop : -0.12 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 231 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.013   0.001   PHE R 120 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8160)
  covalent geometry    : angle       0.53720 (11075)
  SS BOND              : bond        0.00236 (    3)
  SS BOND              : angle       1.07994 (    6)
  hydrogen bonds       : bond        0.03828 (  427)
  hydrogen bonds       : angle       4.37869 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6895 (mm-30)
REVERT: A  274 ASP cc_start: 0.8018 (t0) cc_final: 0.7759 (t0)
REVERT: A  292 ASN cc_start: 0.8577 (t0) cc_final: 0.8203 (t0)
REVERT: A  300 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7322 (mtpt)
REVERT: B   13 GLN cc_start: 0.7884 (pp30) cc_final: 0.7599 (pp30)
REVERT: B   23 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8251 (ttpt)
REVERT: B   59 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8113 (t80)
REVERT: B   61 MET cc_start: 0.8351 (ppp) cc_final: 0.7929 (ppp)
REVERT: B   87 THR cc_start: 0.8383 (m) cc_final: 0.8033 (t)
REVERT: B   98 SER cc_start: 0.8526 (m) cc_final: 0.8256 (p)
REVERT: B  188 MET cc_start: 0.7718 (mmm) cc_final: 0.7502 (mmm)
REVERT: B  230 ASN cc_start: 0.8392 (m-40) cc_final: 0.7989 (m-40)
REVERT: B  234 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8308 (m-80)
REVERT: B  258 ASP cc_start: 0.8117 (t70) cc_final: 0.7241 (t0)
REVERT: B  277 SER cc_start: 0.8332 (p) cc_final: 0.7836 (m)
REVERT: B  289 TYR cc_start: 0.8737 (m-80) cc_final: 0.8209 (m-80)
REVERT: G   20 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7836 (mtmm)
REVERT: G   27 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.8201 (mtt-85)
REVERT: N  120 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8248 (mm-40)
REVERT: R   57 GLU cc_start: 0.7607 (tt0) cc_final: 0.7397 (tt0)
REVERT: R   61 VAL cc_start: 0.8375 (p) cc_final: 0.8122 (t)
REVERT: R  118 MET cc_start: 0.8322 (ttm) cc_final: 0.7905 (mtt)
REVERT: R  209 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7945 (mtp)
REVERT: R  249 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (tt)
REVERT: R  291 MET cc_start: 0.8213 (mmt) cc_final: 0.8002 (mmp)
  outliers start: 22
  outliers final: 15
  residues processed: 219
  average time/residue: 0.1400
  time to fit residues: 37.7398
Evaluate side-chains
  233 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 213
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  296 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 42 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.130367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.113586 restraints weight = 11468.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.09
r_work: 0.3263 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.5240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8163  Z= 0.146
  Angle     :  0.545  10.933  11081  Z= 0.281
  Chirality :  0.040   0.132   1275
  Planarity :  0.004   0.040   1411
  Dihedral  :  4.174  21.625   1123
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.45 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.07 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 aren not related in a simple way.
  whole:  1.24 (0.27), residues: 1021
  helix:  2.23 (0.25), residues: 401
  sheet:  0.12 (0.33), residues: 224
  loop : -0.16 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 231 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.014   0.001   PHE R 120 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8160)
  covalent geometry    : angle       0.54460 (11075)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       1.04021 (    6)
  hydrogen bonds       : bond        0.03892 (  427)
  hydrogen bonds       : angle       4.39130 ( 1221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2366.92 seconds
wall clock time: 41 minutes 12.25 seconds (2472.25 seconds total)