Starting phenix.real_space_refine
on Tue Mar  3 21:33:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xw9_33494/03_2026/7xw9_33494.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xw9_33494/03_2026/7xw9_33494.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xw9_33494/03_2026/7xw9_33494.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xw9_33494/03_2026/7xw9_33494.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xw9_33494/03_2026/7xw9_33494.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xw9_33494/03_2026/7xw9_33494.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5729      2.51       5
     N    1533      2.21       5
     O    1663      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8988
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2294
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1862
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "S"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 25
          Classifications: {'peptide': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.89, per 1000 atoms: 0.21
  Number of scatterers: 8988
  At special positions: 0
  Unit cell: (116.61, 111.54, 123.708, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1663      8.00
     N    1533      7.00
     C    5729      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 317.0 milliseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      37.9% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'R' and resid 23 through 53
    Processing helix  chain 'R' and resid 58 through 79
    Processing helix  chain 'R' and resid 79 through 89
      removed outlier: 3.782A  pdb=" N   ILE R  83 " --> pdb=" O   GLY R  79 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR R  84 " --> pdb=" O   LEU R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 129
      removed outlier: 4.031A  pdb=" N   SER R 113 " --> pdb=" O   ILE R 109 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 162
      removed outlier: 3.837A  pdb=" N   TYR R 156 " --> pdb=" O   PHE R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 184 through 187
    Processing helix  chain 'R' and resid 188 through 220
      Proline residue:  R 203  - end of helix
      removed outlier: 3.553A  pdb=" N   LEU R 220 " --> pdb=" O   ARG R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 258 through 290
      removed outlier: 4.051A  pdb=" N   GLN R 263 " --> pdb=" O   SER R 259 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL R 264 " --> pdb=" O   SER R 260 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   THR R 265 " --> pdb=" O   ARG R 261 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS R 266 " --> pdb=" O   LYS R 262 " (cutoff:3.500A)
      Proline residue:  R 281  - end of helix
      removed outlier: 3.648A  pdb=" N   SER R 290 " --> pdb=" O   VAL R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 321
      Proline residue:  R 317  - end of helix
    Processing helix  chain 'R' and resid 325 through 335
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 4.143A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 4.236A  pdb=" N   GLY A  45 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 264
      removed outlier: 3.733A  pdb=" N   GLN A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ASN A 264 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 293
    Processing helix  chain 'A' and resid 308 through 319
      removed outlier: 3.903A  pdb=" N   LEU A 312 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY A 319 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 327
      removed outlier: 4.067A  pdb=" N   TYR A 326 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 366
      removed outlier: 3.542A  pdb=" N   THR A 350 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 406
      removed outlier: 3.560A  pdb=" N   ARG A 404 " --> pdb=" O   GLN A 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.592A  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 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.550A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.517A  pdb=" N   ASP S 211 " --> pdb=" O   GLU S 208 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 208 through 212'
    Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 239
      removed outlier: 4.631A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 270 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   VAL A 272 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ASP A 274 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.508A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.665A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.843A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.552A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.729A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.414A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.890A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.513A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.978A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.635A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.482A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    453 hydrogen bonds defined for protein.
    1272 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: 1.12

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 1449
        1.30 -     1.43: 2504
        1.43 -     1.57: 5132
        1.57 -     1.70: 0
        1.70 -     1.83: 91
  Bond restraints: 9176
  Sorted by residual:
  bond pdb=" CG  PCA L   1 "
       pdb=" CD  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.517  1.420  0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" CA  HIS L   2 "
       pdb=" C   HIS L   2 "
    ideal  model  delta    sigma   weight residual
    1.525  1.424  0.101 2.10e-02 2.27e+03 2.29e+01
  bond pdb=" N   PCA L   1 "
       pdb=" CD  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.345  1.253  0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" N   PCA L   1 "
       pdb=" CA  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.379  0.079 1.90e-02 2.77e+03 1.73e+01
  bond pdb=" CA  PCA L   1 "
       pdb=" CB  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.530  1.456  0.074 2.00e-02 2.50e+03 1.37e+01
  ... (remaining 9171 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 12332
        2.96 -     5.92: 88
        5.92 -     8.88: 12
        8.88 -    11.84: 1
       11.84 -    14.80: 1
  Bond angle restraints: 12434
  Sorted by residual:
  angle pdb=" N   SER A  44 "
        pdb=" CA  SER A  44 "
        pdb=" C   SER A  44 "
      ideal   model   delta    sigma   weight residual
     111.28  126.08  -14.80 1.09e+00 8.42e-01 1.84e+02
  angle pdb=" C   VAL R 201 "
        pdb=" N   VAL R 202 "
        pdb=" CA  VAL R 202 "
      ideal   model   delta    sigma   weight residual
     122.13  113.55    8.58 1.85e+00 2.92e-01 2.15e+01
  angle pdb=" C   GLU A  43 "
        pdb=" N   SER A  44 "
        pdb=" CA  SER A  44 "
      ideal   model   delta    sigma   weight residual
     120.28  126.31   -6.03 1.34e+00 5.57e-01 2.02e+01
  angle pdb=" N   TRP R 300 "
        pdb=" CA  TRP R 300 "
        pdb=" C   TRP R 300 "
      ideal   model   delta    sigma   weight residual
     114.56  109.00    5.56 1.27e+00 6.20e-01 1.92e+01
  angle pdb=" N   PCA L   1 "
        pdb=" CA  PCA L   1 "
        pdb=" CB  PCA L   1 "
      ideal   model   delta    sigma   weight residual
     110.50  103.75    6.75 1.70e+00 3.46e-01 1.58e+01
  ... (remaining 12429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 4916
       15.42 -    30.85: 426
       30.85 -    46.27: 85
       46.27 -    61.70: 18
       61.70 -    77.12: 6
  Dihedral angle restraints: 5451
    sinusoidal: 2129
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  LEU R  22 "
           pdb=" C   LEU R  22 "
           pdb=" N   GLU R  23 "
           pdb=" CA  GLU R  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.11   23.89     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  TYR S 101 "
           pdb=" C   TYR S 101 "
           pdb=" N   TYR S 102 "
           pdb=" CA  TYR S 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.82   20.18     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  GLU R 298 "
           pdb=" C   GLU R 298 "
           pdb=" N   ASN R 299 "
           pdb=" CA  ASN R 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.53   18.47     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 5448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1300
       0.092 -    0.184: 102
       0.184 -    0.276: 3
       0.276 -    0.369: 1
       0.369 -    0.461: 2
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  SER A  44 "
            pdb=" N   SER A  44 "
            pdb=" C   SER A  44 "
            pdb=" CB  SER A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.31e+00
  chirality pdb=" CA  PRO L   3 "
            pdb=" N   PRO L   3 "
            pdb=" C   PRO L   3 "
            pdb=" CB  PRO L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.30    0.42 2.00e-01 2.50e+01 4.38e+00
  chirality pdb=" CB  VAL R 202 "
            pdb=" CA  VAL R 202 "
            pdb=" CG1 VAL R 202 "
            pdb=" CG2 VAL R 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   PCA L   1 "   -0.064 2.00e-02 2.50e+03   4.54e-02 2.58e+01
        pdb=" CA  PCA L   1 "    0.057 2.00e-02 2.50e+03
        pdb=" CG  PCA L   1 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD  PCA L   1 "   -0.016 2.00e-02 2.50e+03
        pdb=" OE  PCA L   1 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 198 "    0.015 2.00e-02 2.50e+03   2.95e-02 8.69e+00
        pdb=" C   VAL R 198 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL R 198 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE R 199 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  40 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   GLY A  40 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   GLY A  40 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A  41 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1570 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 319
        2.71 -     3.26: 8460
        3.26 -     3.81: 14220
        3.81 -     4.35: 18140
        4.35 -     4.90: 31421
  Nonbonded interactions: 72560
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" NZ  LYS A 308 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OE1 GLU A 234 "
            pdb=" NE2 HIS A 245 "
     model   vdw
     2.326 3.120
  ... (remaining 72555 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
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      :  0.005   0.104   9179  Z= 0.268
  Angle     :  0.682  14.803  12438  Z= 0.391
  Chirality :  0.050   0.461   1408
  Planarity :  0.005   0.064   1573
  Dihedral  : 12.265  77.123   3305
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.25), residues: 1124
  helix:  0.43 (0.26), residues: 384
  sheet:  1.23 (0.32), residues: 272
  loop : -0.41 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B  22 
 TYR   0.021   0.002   TYR R  24 
 PHE   0.021   0.002   PHE R 161 
 TRP   0.020   0.001   TRP R  91 
 HIS   0.011   0.001   HIS L   2 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 9176)
  covalent geometry    : angle       0.68034 (12434)
  SS BOND              : bond        0.00500 (    2)
  SS BOND              : angle       2.65471 (    4)
  hydrogen bonds       : bond        0.16642 (  453)
  hydrogen bonds       : angle       6.83606 ( 1272)
  Misc. bond           : bond        0.08909 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.267 
Fit side-chains
REVERT: R  139 PHE cc_start: 0.8130 (t80) cc_final: 0.7128 (t80)
REVERT: R  147 ILE cc_start: 0.8123 (pt) cc_final: 0.7897 (mt)
REVERT: A   32 ARG cc_start: 0.6777 (mmt90) cc_final: 0.6501 (mmt90)
REVERT: A  314 GLU cc_start: 0.6772 (mp0) cc_final: 0.6408 (mp0)
REVERT: A  329 GLU cc_start: 0.6658 (mp0) cc_final: 0.6429 (mp0)
REVERT: A  396 ASP cc_start: 0.6708 (m-30) cc_final: 0.6473 (m-30)
REVERT: B  175 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7295 (mm-40)
REVERT: B  258 ASP cc_start: 0.6670 (t70) cc_final: 0.6390 (t70)
REVERT: B  340 ASN cc_start: 0.7571 (t0) cc_final: 0.7093 (t0)
REVERT: S   57 THR cc_start: 0.8332 (p) cc_final: 0.8104 (t)
  outliers start: 0
  outliers final: 1
  residues processed: 242
  average time/residue: 0.5302
  time to fit residues: 136.4725
Evaluate side-chains
  227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0170
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
R  61 ASN
A 400 GLN
A 402 ASN
B 176 GLN
B 259 GLN
B 293 ASN
S 167 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115921 restraints weight = 11862.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.75
r_work: 0.3378 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9179  Z= 0.126
  Angle     :  0.566  10.081  12438  Z= 0.300
  Chirality :  0.043   0.201   1408
  Planarity :  0.004   0.048   1573
  Dihedral  :  4.497  37.280   1254
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.06 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.26), residues: 1124
  helix:  1.52 (0.26), residues: 383
  sheet:  1.20 (0.31), residues: 309
  loop : -0.31 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  22 
 TYR   0.015   0.001   TYR R  24 
 PHE   0.020   0.001   PHE R 161 
 TRP   0.016   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9176)
  covalent geometry    : angle       0.56509 (12434)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       1.78558 (    4)
  hydrogen bonds       : bond        0.04410 (  453)
  hydrogen bonds       : angle       5.07626 ( 1272)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 226
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: R  141 ARG cc_start: 0.8068 (ttt-90) cc_final: 0.7826 (ttt180)
REVERT: R  146 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8173 (mp)
REVERT: R  147 ILE cc_start: 0.8262 (pt) cc_final: 0.8014 (mt)
REVERT: R  202 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (t)
REVERT: R  315 ILE cc_start: 0.8408 (mt) cc_final: 0.8187 (mp)
REVERT: A  243 ASN cc_start: 0.8819 (m-40) cc_final: 0.8416 (m110)
REVERT: A  329 GLU cc_start: 0.7169 (mp0) cc_final: 0.6850 (mp0)
REVERT: A  375 TYR cc_start: 0.8576 (m-80) cc_final: 0.8303 (m-80)
REVERT: A  396 ASP cc_start: 0.7511 (m-30) cc_final: 0.7238 (m-30)
REVERT: B  175 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7881 (mm-40)
REVERT: B  258 ASP cc_start: 0.7348 (t70) cc_final: 0.6969 (t70)
REVERT: B  340 ASN cc_start: 0.7794 (t0) cc_final: 0.7535 (t0)
REVERT: S  128 MET cc_start: 0.8531 (mmm) cc_final: 0.8258 (mmm)
  outliers start: 19
  outliers final: 6
  residues processed: 235
  average time/residue: 0.5565
  time to fit residues: 138.6131
Evaluate side-chains
  222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 214
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 37 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 89 optimal weight:    0.4980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 402 ASN
B 259 GLN
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.131856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.114805 restraints weight = 11791.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.74
r_work: 0.3355 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9179  Z= 0.149
  Angle     :  0.566  11.473  12438  Z= 0.299
  Chirality :  0.043   0.197   1408
  Planarity :  0.004   0.047   1573
  Dihedral  :  4.605  44.309   1254
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.33 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.26), residues: 1124
  helix:  1.80 (0.27), residues: 383
  sheet:  1.27 (0.31), residues: 296
  loop : -0.37 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.014   0.002   TYR S 178 
 PHE   0.012   0.001   PHE R 296 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9176)
  covalent geometry    : angle       0.56533 (12434)
  SS BOND              : bond        0.00341 (    2)
  SS BOND              : angle       1.62033 (    4)
  hydrogen bonds       : bond        0.04441 (  453)
  hydrogen bonds       : angle       4.93633 ( 1272)
  Misc. bond           : bond        0.00060 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: R  146 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8161 (mp)
REVERT: R  147 ILE cc_start: 0.8276 (pt) cc_final: 0.8016 (mt)
REVERT: R  202 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7986 (t)
REVERT: A  243 ASN cc_start: 0.8757 (m-40) cc_final: 0.8354 (m-40)
REVERT: A  273 VAL cc_start: 0.8828 (t) cc_final: 0.8621 (p)
REVERT: A  329 GLU cc_start: 0.7178 (mp0) cc_final: 0.6643 (mp0)
REVERT: A  375 TYR cc_start: 0.8603 (m-80) cc_final: 0.8334 (m-80)
REVERT: A  389 ARG cc_start: 0.8250 (mtm180) cc_final: 0.8034 (mtm180)
REVERT: A  396 ASP cc_start: 0.7551 (m-30) cc_final: 0.7240 (m-30)
REVERT: B   22 ARG cc_start: 0.7433 (mtt90) cc_final: 0.6930 (mmm-85)
REVERT: B  175 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7867 (mm-40)
REVERT: B  258 ASP cc_start: 0.7377 (t70) cc_final: 0.6882 (t70)
REVERT: B  340 ASN cc_start: 0.7885 (t0) cc_final: 0.7665 (t160)
REVERT: S   18 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7821 (ttt180)
REVERT: S   67 ARG cc_start: 0.8155 (ptm-80) cc_final: 0.7836 (ptm-80)
REVERT: S  128 MET cc_start: 0.8539 (mmm) cc_final: 0.8234 (mmm)
  outliers start: 25
  outliers final: 14
  residues processed: 229
  average time/residue: 0.6256
  time to fit residues: 151.3216
Evaluate side-chains
  229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 213
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 402 ASN
B 259 GLN
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.129290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111985 restraints weight = 12013.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.77
r_work: 0.3312 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   9179  Z= 0.265
  Angle     :  0.647  11.476  12438  Z= 0.344
  Chirality :  0.047   0.217   1408
  Planarity :  0.005   0.052   1573
  Dihedral  :  5.010  42.581   1252
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.76 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.26), residues: 1124
  helix:  1.64 (0.27), residues: 384
  sheet:  1.05 (0.30), residues: 308
  loop : -0.46 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 306 
 TYR   0.027   0.002   TYR B 105 
 PHE   0.017   0.002   PHE R 296 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.008   0.002   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 ( 9176)
  covalent geometry    : angle       0.64590 (12434)
  SS BOND              : bond        0.00824 (    2)
  SS BOND              : angle       1.82282 (    4)
  hydrogen bonds       : bond        0.05384 (  453)
  hydrogen bonds       : angle       5.16997 ( 1272)
  Misc. bond           : bond        0.00116 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 219
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: R  146 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8213 (mp)
REVERT: R  147 ILE cc_start: 0.8318 (pt) cc_final: 0.8079 (mt)
REVERT: R  161 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5800 (t80)
REVERT: A  243 ASN cc_start: 0.8820 (m-40) cc_final: 0.8369 (m110)
REVERT: A  329 GLU cc_start: 0.7297 (mp0) cc_final: 0.6935 (mp0)
REVERT: A  375 TYR cc_start: 0.8624 (m-80) cc_final: 0.8334 (m-80)
REVERT: A  389 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7799 (mtt180)
REVERT: A  396 ASP cc_start: 0.7640 (m-30) cc_final: 0.7348 (m-30)
REVERT: B   22 ARG cc_start: 0.7655 (mtt90) cc_final: 0.7199 (mmm-85)
REVERT: B   45 MET cc_start: 0.8722 (mtt) cc_final: 0.8482 (mtm)
REVERT: B  258 ASP cc_start: 0.7531 (t70) cc_final: 0.7116 (t70)
REVERT: B  340 ASN cc_start: 0.8063 (t0) cc_final: 0.7856 (t160)
REVERT: S  128 MET cc_start: 0.8593 (mmm) cc_final: 0.8298 (mmm)
REVERT: S  201 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8105 (m)
  outliers start: 29
  outliers final: 19
  residues processed: 230
  average time/residue: 0.6254
  time to fit residues: 151.8931
Evaluate side-chains
  231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 209
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 PHE
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 293 ASN
A 400 GLN
B  35 ASN
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.131532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114304 restraints weight = 11995.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.77
r_work: 0.3347 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9179  Z= 0.139
  Angle     :  0.557  10.845  12438  Z= 0.296
  Chirality :  0.043   0.203   1408
  Planarity :  0.004   0.046   1573
  Dihedral  :  4.641  41.903   1252
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.10 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1124
  helix:  1.86 (0.27), residues: 384
  sheet:  1.03 (0.30), residues: 307
  loop : -0.44 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.013   0.001   TYR S 101 
 PHE   0.013   0.001   PHE R 296 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9176)
  covalent geometry    : angle       0.55620 (12434)
  SS BOND              : bond        0.00376 (    2)
  SS BOND              : angle       1.50956 (    4)
  hydrogen bonds       : bond        0.04262 (  453)
  hydrogen bonds       : angle       4.92975 ( 1272)
  Misc. bond           : bond        0.00061 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 217
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: R  146 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8185 (mp)
REVERT: R  147 ILE cc_start: 0.8304 (pt) cc_final: 0.8049 (mt)
REVERT: R  202 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (t)
REVERT: A    8 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7245 (mt-10)
REVERT: A  243 ASN cc_start: 0.8789 (m-40) cc_final: 0.8427 (m-40)
REVERT: A  329 GLU cc_start: 0.7226 (mp0) cc_final: 0.6878 (mp0)
REVERT: A  375 TYR cc_start: 0.8628 (m-80) cc_final: 0.8348 (m-80)
REVERT: A  379 THR cc_start: 0.8379 (p) cc_final: 0.8077 (m)
REVERT: A  396 ASP cc_start: 0.7618 (m-30) cc_final: 0.7308 (m-30)
REVERT: B   22 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7117 (mtt90)
REVERT: B   45 MET cc_start: 0.8690 (mtt) cc_final: 0.8456 (mtm)
REVERT: B  175 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7948 (mm-40)
REVERT: B  212 ASP cc_start: 0.8166 (p0) cc_final: 0.7816 (p0)
REVERT: B  258 ASP cc_start: 0.7495 (t70) cc_final: 0.6940 (t70)
REVERT: B  340 ASN cc_start: 0.7864 (t0) cc_final: 0.7632 (t160)
REVERT: S   18 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7748 (ttt180)
REVERT: S  128 MET cc_start: 0.8540 (mmm) cc_final: 0.8213 (mmm)
REVERT: S  167 GLN cc_start: 0.8563 (tt0) cc_final: 0.8341 (tt0)
  outliers start: 25
  outliers final: 17
  residues processed: 228
  average time/residue: 0.6616
  time to fit residues: 159.1061
Evaluate side-chains
  233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 214
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0970
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 245 HIS
A 400 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.132475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.115228 restraints weight = 11985.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 1.77
r_work: 0.3364 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9179  Z= 0.119
  Angle     :  0.542  10.724  12438  Z= 0.285
  Chirality :  0.042   0.200   1408
  Planarity :  0.004   0.043   1573
  Dihedral  :  4.476  44.332   1252
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.92 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.26), residues: 1124
  helix:  2.12 (0.27), residues: 378
  sheet:  0.96 (0.30), residues: 303
  loop : -0.35 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.021   0.001   TYR S 101 
 PHE   0.013   0.001   PHE R 139 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS L   2 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9176)
  covalent geometry    : angle       0.54194 (12434)
  SS BOND              : bond        0.00270 (    2)
  SS BOND              : angle       1.41622 (    4)
  hydrogen bonds       : bond        0.03941 (  453)
  hydrogen bonds       : angle       4.80979 ( 1272)
  Misc. bond           : bond        0.00054 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 219
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: R   30 LEU cc_start: 0.7596 (mt) cc_final: 0.7341 (mm)
REVERT: R  122 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7604 (mt-10)
REVERT: R  147 ILE cc_start: 0.8297 (pt) cc_final: 0.8030 (mt)
REVERT: R  202 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.8012 (t)
REVERT: A  329 GLU cc_start: 0.7188 (mp0) cc_final: 0.6847 (mp0)
REVERT: A  375 TYR cc_start: 0.8632 (m-80) cc_final: 0.8324 (m-80)
REVERT: A  379 THR cc_start: 0.8324 (p) cc_final: 0.8044 (m)
REVERT: A  396 ASP cc_start: 0.7588 (m-30) cc_final: 0.7281 (m-30)
REVERT: B   22 ARG cc_start: 0.7478 (mtt90) cc_final: 0.7038 (mtt90)
REVERT: B   45 MET cc_start: 0.8688 (mtt) cc_final: 0.8448 (mtm)
REVERT: B  175 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7961 (mm-40)
REVERT: B  184 THR cc_start: 0.8317 (p) cc_final: 0.7993 (m)
REVERT: B  212 ASP cc_start: 0.8168 (p0) cc_final: 0.7789 (p0)
REVERT: B  258 ASP cc_start: 0.7467 (t70) cc_final: 0.6916 (t70)
REVERT: B  340 ASN cc_start: 0.7842 (t0) cc_final: 0.7610 (t160)
REVERT: S   18 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7774 (ttt180)
REVERT: S  128 MET cc_start: 0.8538 (mmm) cc_final: 0.8311 (mmm)
REVERT: S  167 GLN cc_start: 0.8554 (tt0) cc_final: 0.8317 (tt0)
  outliers start: 28
  outliers final: 17
  residues processed: 232
  average time/residue: 0.6444
  time to fit residues: 157.8806
Evaluate side-chains
  229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 211
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0870
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 245 HIS
A 400 GLN
B 259 GLN
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.132474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115177 restraints weight = 12004.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.78
r_work: 0.3356 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9179  Z= 0.126
  Angle     :  0.543  10.773  12438  Z= 0.287
  Chirality :  0.042   0.204   1408
  Planarity :  0.004   0.041   1573
  Dihedral  :  4.438  42.590   1252
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.63 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.26), residues: 1124
  helix:  2.19 (0.27), residues: 378
  sheet:  0.99 (0.30), residues: 301
  loop : -0.37 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 404 
 TYR   0.012   0.001   TYR S 178 
 PHE   0.011   0.001   PHE R 296 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9176)
  covalent geometry    : angle       0.54259 (12434)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       1.44028 (    4)
  hydrogen bonds       : bond        0.04003 (  453)
  hydrogen bonds       : angle       4.80709 ( 1272)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: R   30 LEU cc_start: 0.7587 (mt) cc_final: 0.7356 (mm)
REVERT: R  122 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7548 (mt-10)
REVERT: R  147 ILE cc_start: 0.8307 (pt) cc_final: 0.7994 (mp)
REVERT: R  176 VAL cc_start: 0.7484 (t) cc_final: 0.7060 (p)
REVERT: R  202 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8030 (t)
REVERT: A   43 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6483 (tt0)
REVERT: A  329 GLU cc_start: 0.7175 (mp0) cc_final: 0.6838 (mp0)
REVERT: A  375 TYR cc_start: 0.8627 (m-80) cc_final: 0.8306 (m-80)
REVERT: A  389 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.8012 (mtm180)
REVERT: A  396 ASP cc_start: 0.7585 (m-30) cc_final: 0.7278 (m-30)
REVERT: B   22 ARG cc_start: 0.7467 (mtt90) cc_final: 0.7061 (mtt90)
REVERT: B   45 MET cc_start: 0.8681 (mtt) cc_final: 0.8443 (mtm)
REVERT: B  175 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7952 (mm-40)
REVERT: B  184 THR cc_start: 0.8346 (p) cc_final: 0.8013 (m)
REVERT: B  212 ASP cc_start: 0.8173 (p0) cc_final: 0.7814 (p0)
REVERT: B  258 ASP cc_start: 0.7408 (t70) cc_final: 0.6852 (t70)
REVERT: B  340 ASN cc_start: 0.7869 (t0) cc_final: 0.7642 (t160)
REVERT: S   18 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7714 (ttt180)
REVERT: S  128 MET cc_start: 0.8535 (mmm) cc_final: 0.8278 (mmm)
REVERT: S  167 GLN cc_start: 0.8570 (tt0) cc_final: 0.8327 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 225
  average time/residue: 0.6091
  time to fit residues: 145.3537
Evaluate side-chains
  234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 210
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0980
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 245 HIS
A 400 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.132655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.115269 restraints weight = 12004.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.78
r_work: 0.3357 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9179  Z= 0.130
  Angle     :  0.545  11.049  12438  Z= 0.288
  Chirality :  0.042   0.206   1408
  Planarity :  0.004   0.041   1573
  Dihedral  :  4.424  42.072   1252
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.73 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.26), residues: 1124
  helix:  2.24 (0.27), residues: 378
  sheet:  0.99 (0.30), residues: 301
  loop : -0.39 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  19 
 TYR   0.012   0.001   TYR S 178 
 PHE   0.011   0.001   PHE R 296 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9176)
  covalent geometry    : angle       0.54422 (12434)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       1.43852 (    4)
  hydrogen bonds       : bond        0.03994 (  453)
  hydrogen bonds       : angle       4.80442 ( 1272)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 211
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: R   30 LEU cc_start: 0.7570 (mt) cc_final: 0.7359 (mm)
REVERT: R  122 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7580 (mt-10)
REVERT: R  147 ILE cc_start: 0.8316 (pt) cc_final: 0.8074 (mt)
REVERT: R  176 VAL cc_start: 0.7532 (t) cc_final: 0.7098 (p)
REVERT: A   43 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6486 (tt0)
REVERT: A  329 GLU cc_start: 0.7173 (mp0) cc_final: 0.6830 (mp0)
REVERT: A  375 TYR cc_start: 0.8641 (m-80) cc_final: 0.8310 (m-80)
REVERT: A  389 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7902 (mtm180)
REVERT: A  396 ASP cc_start: 0.7596 (m-30) cc_final: 0.7278 (m-30)
REVERT: B   22 ARG cc_start: 0.7530 (mtt90) cc_final: 0.7122 (mmm-85)
REVERT: B   45 MET cc_start: 0.8696 (mtt) cc_final: 0.8453 (mtm)
REVERT: B  175 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7948 (mm-40)
REVERT: B  184 THR cc_start: 0.8298 (p) cc_final: 0.8005 (m)
REVERT: B  212 ASP cc_start: 0.8171 (p0) cc_final: 0.7833 (p0)
REVERT: B  258 ASP cc_start: 0.7402 (t70) cc_final: 0.6977 (t70)
REVERT: B  340 ASN cc_start: 0.7889 (t0) cc_final: 0.7668 (t160)
REVERT: S   18 ARG cc_start: 0.8070 (ttm170) cc_final: 0.7710 (ttt180)
REVERT: S   72 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7690 (ptm-80)
REVERT: S  128 MET cc_start: 0.8537 (mmm) cc_final: 0.8271 (mmm)
REVERT: S  167 GLN cc_start: 0.8576 (tt0) cc_final: 0.8297 (tt0)
  outliers start: 27
  outliers final: 22
  residues processed: 225
  average time/residue: 0.5790
  time to fit residues: 137.9247
Evaluate side-chains
  233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  280 MET
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.132446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.115038 restraints weight = 11931.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.78
r_work: 0.3352 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9179  Z= 0.135
  Angle     :  0.543  11.147  12438  Z= 0.287
  Chirality :  0.042   0.132   1408
  Planarity :  0.004   0.040   1573
  Dihedral  :  4.421  41.527   1252
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.53 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.26), residues: 1124
  helix:  2.19 (0.27), residues: 379
  sheet:  1.01 (0.30), residues: 302
  loop : -0.40 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  19 
 TYR   0.012   0.001   TYR S 178 
 PHE   0.011   0.001   PHE R 296 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9176)
  covalent geometry    : angle       0.54198 (12434)
  SS BOND              : bond        0.00366 (    2)
  SS BOND              : angle       1.45123 (    4)
  hydrogen bonds       : bond        0.04040 (  453)
  hydrogen bonds       : angle       4.81337 ( 1272)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 213
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: R   30 LEU cc_start: 0.7580 (mt) cc_final: 0.7374 (mm)
REVERT: R  122 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7585 (mt-10)
REVERT: R  147 ILE cc_start: 0.8317 (pt) cc_final: 0.8086 (mt)
REVERT: R  176 VAL cc_start: 0.7536 (t) cc_final: 0.7112 (p)
REVERT: A   43 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6496 (tt0)
REVERT: A  329 GLU cc_start: 0.7174 (mp0) cc_final: 0.6832 (mp0)
REVERT: A  375 TYR cc_start: 0.8642 (m-80) cc_final: 0.8300 (m-80)
REVERT: A  396 ASP cc_start: 0.7617 (m-30) cc_final: 0.7304 (m-30)
REVERT: B   22 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7284 (mmm-85)
REVERT: B   45 MET cc_start: 0.8684 (mtt) cc_final: 0.8441 (mtm)
REVERT: B  175 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7962 (mm-40)
REVERT: B  184 THR cc_start: 0.8316 (p) cc_final: 0.8022 (m)
REVERT: B  212 ASP cc_start: 0.8170 (p0) cc_final: 0.7841 (p0)
REVERT: B  340 ASN cc_start: 0.7888 (t0) cc_final: 0.7666 (t160)
REVERT: S   18 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7785 (ttt180)
REVERT: S   43 LYS cc_start: 0.7743 (mppt) cc_final: 0.7310 (mppt)
REVERT: S   72 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7707 (ptm-80)
REVERT: S  128 MET cc_start: 0.8529 (mmm) cc_final: 0.8262 (mmm)
REVERT: S  167 GLN cc_start: 0.8576 (tt0) cc_final: 0.8291 (tt0)
  outliers start: 31
  outliers final: 27
  residues processed: 227
  average time/residue: 0.5928
  time to fit residues: 142.5442
Evaluate side-chains
  242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 213
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  280 MET
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.131697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114288 restraints weight = 11911.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.77
r_work: 0.3341 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9179  Z= 0.162
  Angle     :  0.572  11.312  12438  Z= 0.303
  Chirality :  0.043   0.140   1408
  Planarity :  0.004   0.041   1573
  Dihedral  :  4.536  41.101   1252
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.63 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.26), residues: 1124
  helix:  2.12 (0.27), residues: 379
  sheet:  0.99 (0.30), residues: 302
  loop : -0.44 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 314 
 TYR   0.012   0.002   TYR S 178 
 PHE   0.012   0.001   PHE R 296 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 9176)
  covalent geometry    : angle       0.57167 (12434)
  SS BOND              : bond        0.00487 (    2)
  SS BOND              : angle       1.50909 (    4)
  hydrogen bonds       : bond        0.04320 (  453)
  hydrogen bonds       : angle       4.88230 ( 1272)
  Misc. bond           : bond        0.00052 (    1)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 213
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: R   30 LEU cc_start: 0.7590 (mt) cc_final: 0.7385 (mm)
REVERT: R  122 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7579 (mt-10)
REVERT: R  147 ILE cc_start: 0.8325 (pt) cc_final: 0.8108 (mt)
REVERT: R  158 MET cc_start: 0.6728 (mtp) cc_final: 0.6491 (mtp)
REVERT: A    8 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7332 (mt-10)
REVERT: A   43 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6480 (tt0)
REVERT: A  329 GLU cc_start: 0.7189 (mp0) cc_final: 0.6847 (mp0)
REVERT: A  375 TYR cc_start: 0.8630 (m-80) cc_final: 0.8313 (m-80)
REVERT: A  396 ASP cc_start: 0.7602 (m-30) cc_final: 0.7285 (m-30)
REVERT: B   22 ARG cc_start: 0.7564 (mtt90) cc_final: 0.7118 (mmm-85)
REVERT: B   45 MET cc_start: 0.8689 (mtt) cc_final: 0.8448 (mtm)
REVERT: B  175 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7961 (mm-40)
REVERT: B  184 THR cc_start: 0.8310 (p) cc_final: 0.8022 (m)
REVERT: B  258 ASP cc_start: 0.7380 (t70) cc_final: 0.6960 (t70)
REVERT: B  340 ASN cc_start: 0.7913 (t0) cc_final: 0.7690 (t160)
REVERT: S   18 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7723 (ttt180)
REVERT: S   43 LYS cc_start: 0.7755 (mppt) cc_final: 0.7265 (mppt)
REVERT: S   72 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7765 (ptp-170)
REVERT: S  128 MET cc_start: 0.8531 (mmm) cc_final: 0.8269 (mmm)
REVERT: S  167 GLN cc_start: 0.8586 (tt0) cc_final: 0.8312 (tt0)
  outliers start: 30
  outliers final: 26
  residues processed: 227
  average time/residue: 0.5846
  time to fit residues: 140.4756
Evaluate side-chains
  241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 213
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  141 ARG
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  280 MET
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 64 optimal weight:    0.3980
   chunk 100 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0570
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
R 297 GLN
A 245 HIS
A 400 GLN
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.133908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.116648 restraints weight = 11797.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.77
r_work: 0.3383 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   9179  Z= 0.108
  Angle     :  0.534  11.140  12438  Z= 0.280
  Chirality :  0.041   0.127   1408
  Planarity :  0.004   0.040   1573
  Dihedral  :  4.273  40.662   1252
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.55 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.26), residues: 1124
  helix:  2.29 (0.27), residues: 378
  sheet:  0.94 (0.30), residues: 304
  loop : -0.39 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 314 
 TYR   0.012   0.001   TYR S 178 
 PHE   0.013   0.001   PHE R 304 
 TRP   0.013   0.001   TRP B 297 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9176)
  covalent geometry    : angle       0.53382 (12434)
  SS BOND              : bond        0.00270 (    2)
  SS BOND              : angle       1.36036 (    4)
  hydrogen bonds       : bond        0.03687 (  453)
  hydrogen bonds       : angle       4.74194 ( 1272)
  Misc. bond           : bond        0.00022 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3778.34 seconds
wall clock time: 64 minutes 53.37 seconds (3893.37 seconds total)