Starting phenix.real_space_refine
on Wed Mar  4 06:44:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bnq_12232/03_2026/7bnq_12232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bnq_12232/03_2026/7bnq_12232.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bnq_12232/03_2026/7bnq_12232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bnq_12232/03_2026/7bnq_12232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bnq_12232/03_2026/7bnq_12232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bnq_12232/03_2026/7bnq_12232.cif"
  }
  resolution = 4.1
  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=   0.004 sd=   0.044
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      32      5.16       5
     C    7323      2.51       5
     N    1983      2.21       5
     O    2279      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 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: 11617
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 761, 6020
          Classifications: {'peptide': 761}
          Link IDs: {'PTRANS': 27, 'TRANS': 733}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2784
          Classifications: {'peptide': 370}
          Link IDs: {'PTRANS': 11, 'TRANS': 358}
    Chain: "C"
      Number of atoms: 408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 408
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 6, 'TRANS': 49}
    Chain: "D"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1760
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
    Chain: "E"
      Number of atoms: 645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 645
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 5, 'TRANS': 77}
  Time building chain proxies: 2.32, per 1000 atoms: 0.20
  Number of scatterers: 11617
  At special positions: 0
  Unit cell: (119.84, 126.26, 99.51, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    2279      8.00
     N    1983      7.00
     C    7323      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 665 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 476.2 milliseconds
  

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2716

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 18 sheets defined
      22.0% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
      removed outlier: 3.646A  pdb=" N   MET A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 65
    Processing helix  chain 'A' and resid 106 through 118
      removed outlier: 3.514A  pdb=" N   LEU A 110 " --> pdb=" O   LYS A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 215 through 231
      removed outlier: 4.268A  pdb=" N   LEU A 219 " --> pdb=" O   GLN A 215 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A 216 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLU A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   THR A 225 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.867A  pdb=" N   GLN A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   LEU A 287 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR A 288 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 316
      removed outlier: 3.840A  pdb=" N   THR A 302 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLY A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 392
    Processing helix  chain 'A' and resid 497 through 500
      removed outlier: 3.728A  pdb=" N   ASP A 500 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 500'
    Processing helix  chain 'A' and resid 543 through 553
      removed outlier: 3.816A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'B' and resid 23 through 27
    Processing helix  chain 'B' and resid 332 through 336
      removed outlier: 4.148A  pdb=" N   GLY B 335 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 38
    Processing helix  chain 'D' and resid 31 through 45
      removed outlier: 3.642A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 62
      removed outlier: 3.714A  pdb=" N   TYR D  62 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
      removed outlier: 3.655A  pdb=" N   VAL D  71 " --> pdb=" O   TYR D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 119
      removed outlier: 3.813A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 124 through 129
      removed outlier: 4.087A  pdb=" N   PHE D 128 " --> pdb=" O   LEU D 124 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLY D 129 " --> pdb=" O   GLN D 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 124 through 129'
    Processing helix  chain 'D' and resid 137 through 154
      removed outlier: 3.798A  pdb=" N   LYS D 149 " --> pdb=" O   SER D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.569A  pdb=" N   LYS D 165 " --> pdb=" O   THR D 161 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR D 177 " --> pdb=" O   ARG D 173 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLU D 178 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   TYR D 184 " --> pdb=" O   SER D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
      removed outlier: 3.566A  pdb=" N   VAL D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLY D 200 " --> pdb=" O   ASN D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 213
    Processing helix  chain 'D' and resid 214 through 224
      removed outlier: 3.711A  pdb=" N   ARG D 223 " --> pdb=" O   GLU D 219 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN D 224 " --> pdb=" O   ASN D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 240
    Processing helix  chain 'E' and resid 41 through 45
    Processing helix  chain 'E' and resid 54 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32
      removed outlier: 7.014A  pdb=" N   ASP A  28 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   VAL A  86 " --> pdb=" O   ASP A  28 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   GLU A  32 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   GLU A  90 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS A  89 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASP A  74 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 99
      removed outlier: 7.308A  pdb=" N   LEU A 165 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   PHE A  99 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.782A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER B 193 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295
      removed outlier: 4.314A  pdb=" N   GLU A 294 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LEU A 337 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   VAL A 339 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 6.022A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   ARG A 350 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 12.929A  pdb=" N   TYR A 416 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 10.279A  pdb=" N   ILE A 352 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 12.715A  pdb=" N   VAL A 418 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 10.141A  pdb=" N   PHE A 354 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 12.157A  pdb=" N   GLU A 420 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 427 through 432
      removed outlier: 3.586A  pdb=" N   ASN A 427 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLY A 443 " --> pdb=" O   ASN A 427 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA A 527 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 525 " --> pdb=" O   PHE A 517 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY A 530 " --> pdb=" O   THR A 571 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 628 " --> pdb=" O   ILE A 719 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68
    Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 102
      removed outlier: 3.767A  pdb=" N   GLU B  99 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLU B 107 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ASP B 101 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   SER B 105 " --> pdb=" O   ASP B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 115 through 117
      removed outlier: 3.649A  pdb=" N   THR B 116 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 162 through 164
      removed outlier: 6.538A  pdb=" N   LEU B 171 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   THR B 184 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ALA B 173 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.676A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 253
      removed outlier: 3.886A  pdb=" N   ALA B 260 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR B 268 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 297
      removed outlier: 6.889A  pdb=" N   ALA B 307 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 345 through 346
      removed outlier: 3.646A  pdb=" N   GLN B 360 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 31 through 35
      removed outlier: 4.332A  pdb=" N   ILE E  32 " --> pdb=" O   GLN E  80 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN E  80 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 72 through 75

    429 hydrogen bonds defined for protein.
    1197 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: 1.73

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3883
        1.34 -     1.46: 2557
        1.46 -     1.58: 5367
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 11869
  Sorted by residual:
  bond pdb=" C   SER B 198 "
       pdb=" N   ALA B 199 "
    ideal  model  delta    sigma   weight residual
    1.335  1.307  0.027 1.41e-02 5.03e+03 3.78e+00
  bond pdb=" C   LEU D  85 "
       pdb=" N   PRO D  86 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.20e-02 6.94e+03 1.34e+00
  bond pdb=" CB  VAL D 194 "
       pdb=" CG2 VAL D 194 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" N   ARG B  77 "
       pdb=" CA  ARG B  77 "
    ideal  model  delta    sigma   weight residual
    1.461  1.478 -0.016 1.49e-02 4.50e+03 1.19e+00
  bond pdb=" CA  VAL B 147 "
       pdb=" CB  VAL B 147 "
    ideal  model  delta    sigma   weight residual
    1.542  1.559 -0.017 1.55e-02 4.16e+03 1.16e+00
  ... (remaining 11864 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.32: 16038
        3.32 -     6.64: 82
        6.64 -     9.96: 11
        9.96 -    13.27: 1
       13.27 -    16.59: 1
  Bond angle restraints: 16133
  Sorted by residual:
  angle pdb=" N   ALA B  78 "
        pdb=" CA  ALA B  78 "
        pdb=" C   ALA B  78 "
      ideal   model   delta    sigma   weight residual
     114.75  108.00    6.75 1.26e+00 6.30e-01 2.87e+01
  angle pdb=" CA  LEU A 450 "
        pdb=" CB  LEU A 450 "
        pdb=" CG  LEU A 450 "
      ideal   model   delta    sigma   weight residual
     116.30  132.89  -16.59 3.50e+00 8.16e-02 2.25e+01
  angle pdb=" C   GLN E  52 "
        pdb=" N   GLN E  53 "
        pdb=" CA  GLN E  53 "
      ideal   model   delta    sigma   weight residual
     121.54  129.63   -8.09 1.91e+00 2.74e-01 1.79e+01
  angle pdb=" CA  LEU A  34 "
        pdb=" CB  LEU A  34 "
        pdb=" CG  LEU A  34 "
      ideal   model   delta    sigma   weight residual
     116.30  129.19  -12.89 3.50e+00 8.16e-02 1.36e+01
  angle pdb=" N   GLY A 443 "
        pdb=" CA  GLY A 443 "
        pdb=" C   GLY A 443 "
      ideal   model   delta    sigma   weight residual
     110.96  115.24   -4.28 1.19e+00 7.06e-01 1.29e+01
  ... (remaining 16128 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6252
       17.91 -    35.82: 626
       35.82 -    53.74: 89
       53.74 -    71.65: 24
       71.65 -    89.56: 16
  Dihedral angle restraints: 7007
    sinusoidal: 2735
      harmonic: 4272
  Sorted by residual:
  dihedral pdb=" CB  CYS A 435 "
           pdb=" SG  CYS A 435 "
           pdb=" SG  CYS A 665 "
           pdb=" CB  CYS A 665 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.17   78.83     1      1.00e+01 1.00e-02 7.74e+01
  dihedral pdb=" CA  GLU B  39 "
           pdb=" C   GLU B  39 "
           pdb=" N   ASN B  40 "
           pdb=" CA  ASN B  40 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.34  -28.66     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" CA  ARG B 243 "
           pdb=" C   ARG B 243 "
           pdb=" N   LEU B 244 "
           pdb=" CA  LEU B 244 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.62   26.38     0      5.00e+00 4.00e-02 2.78e+01
  ... (remaining 7004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1226
       0.049 -    0.098: 422
       0.098 -    0.148: 105
       0.148 -    0.197: 10
       0.197 -    0.246: 2
  Chirality restraints: 1765
  Sorted by residual:
  chirality pdb=" CB  VAL D 108 "
            pdb=" CA  VAL D 108 "
            pdb=" CG1 VAL D 108 "
            pdb=" CG2 VAL D 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  VAL C  76 "
            pdb=" N   VAL C  76 "
            pdb=" C   VAL C  76 "
            pdb=" CB  VAL C  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  ILE B 290 "
            pdb=" CA  ILE B 290 "
            pdb=" CG1 ILE B 290 "
            pdb=" CG2 ILE B 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.93e-01
  ... (remaining 1762 not shown)

  Planarity restraints: 2123
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 215 "   -0.047 5.00e-02 4.00e+02   7.03e-02 7.91e+00
        pdb=" N   PRO D 216 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO D 216 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO D 216 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 248 "   -0.044 5.00e-02 4.00e+02   6.58e-02 6.94e+00
        pdb=" N   PRO A 249 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 249 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 249 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 778 "   -0.038 5.00e-02 4.00e+02   5.79e-02 5.37e+00
        pdb=" N   PRO A 779 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 779 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 779 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 2120 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3538
        2.81 -     3.34: 9686
        3.34 -     3.86: 18519
        3.86 -     4.38: 19231
        4.38 -     4.90: 34266
  Nonbonded interactions: 85240
  Sorted by model distance:
  nonbonded pdb=" O   SER B 112 "
            pdb=" OG  SER B 112 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG1 THR E  72 "
            pdb=" O   LEU E  93 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LEU D 119 "
            pdb=" OG  SER D 122 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   ASN A 113 "
            pdb=" OG  SER A 117 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   GLU B 150 "
            pdb=" OG1 THR B 166 "
     model   vdw
     2.318 3.040
  ... (remaining 85235 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.140
  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:             0.020
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     10.590
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
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   0.049  11870  Z= 0.224
  Angle     :  0.799  16.592  16135  Z= 0.445
  Chirality :  0.052   0.246   1765
  Planarity :  0.006   0.070   2123
  Dihedral  : 14.886  89.562   4288
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.27 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.83 (0.18), residues: 1476
  helix: -2.58 (0.20), residues: 286
  sheet: -1.96 (0.23), residues: 430
  loop : -2.90 (0.18), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 366 
 TYR   0.024   0.002   TYR A 578 
 PHE   0.019   0.002   PHE A 517 
 TRP   0.022   0.002   TRP A 776 
 HIS   0.005   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (11869)
  covalent geometry    : angle       0.79916 (16133)
  SS BOND              : bond        0.00328 (    1)
  SS BOND              : angle       0.78565 (    2)
  hydrogen bonds       : bond        0.12364 (  429)
  hydrogen bonds       : angle       5.97858 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 194
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.6075 (ptt) cc_final: 0.5508 (ptt)
REVERT: A  123 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7657 (mp0)
REVERT: A  142 TYR cc_start: 0.8896 (m-10) cc_final: 0.7928 (m-80)
REVERT: A  164 ASP cc_start: 0.8496 (m-30) cc_final: 0.8271 (m-30)
REVERT: A  208 VAL cc_start: 0.9182 (t) cc_final: 0.8821 (p)
REVERT: A  272 GLU cc_start: 0.8057 (tt0) cc_final: 0.7618 (tt0)
REVERT: A  380 ASP cc_start: 0.8463 (p0) cc_final: 0.7938 (p0)
REVERT: A  512 ASP cc_start: 0.7874 (m-30) cc_final: 0.7548 (p0)
REVERT: A  552 MET cc_start: 0.9370 (mmm) cc_final: 0.8661 (tpp)
REVERT: B  127 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8236 (mm-30)
REVERT: B  298 LEU cc_start: 0.9420 (pt) cc_final: 0.9220 (pt)
REVERT: C   30 ARG cc_start: 0.6363 (ttt-90) cc_final: 0.5630 (ttm170)
REVERT: D  117 MET cc_start: 0.9047 (ttp) cc_final: 0.8845 (ttm)
REVERT: D  178 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8360 (mm-30)
REVERT: D  201 MET cc_start: 0.9137 (mtp) cc_final: 0.8896 (ttm)
REVERT: D  237 ILE cc_start: 0.9364 (tt) cc_final: 0.9120 (tt)
REVERT: E   34 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8657 (mm110)
REVERT: E   36 ASN cc_start: 0.8288 (t0) cc_final: 0.7798 (t0)
REVERT: E   74 PHE cc_start: 0.8824 (m-80) cc_final: 0.8411 (m-10)
REVERT: E  105 ASP cc_start: 0.9014 (t0) cc_final: 0.8677 (t0)
  outliers start: 4
  outliers final: 4
  residues processed: 198
  average time/residue: 0.1165
  time to fit residues: 32.0496
Evaluate side-chains
  130 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
A 196 HIS
A 371 GLN
** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  64 HIS
B 334 ASN
B 336 ASN
D  40 GLN
D  41 GLN
D  60 ASN
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.103051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.076447 restraints weight = 28550.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.078781 restraints weight = 16759.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.080371 restraints weight = 11753.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.081263 restraints weight = 9249.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.082136 restraints weight = 7936.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11870  Z= 0.169
  Angle     :  0.602   7.967  16135  Z= 0.320
  Chirality :  0.044   0.154   1765
  Planarity :  0.005   0.060   2123
  Dihedral  :  5.344  24.250   1628
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.77 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.93 (0.20), residues: 1476
  helix: -0.81 (0.27), residues: 295
  sheet: -1.63 (0.25), residues: 411
  loop : -2.63 (0.20), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 127 
 TYR   0.020   0.002   TYR A 578 
 PHE   0.014   0.001   PHE A 517 
 TRP   0.018   0.001   TRP A 776 
 HIS   0.004   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (11869)
  covalent geometry    : angle       0.60202 (16133)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       1.90500 (    2)
  hydrogen bonds       : bond        0.03875 (  429)
  hydrogen bonds       : angle       5.06683 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5842 (ptt) cc_final: 0.5487 (ptt)
REVERT: A  123 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7416 (mp0)
REVERT: A  142 TYR cc_start: 0.8981 (m-10) cc_final: 0.8095 (m-80)
REVERT: A  171 GLU cc_start: 0.8117 (pp20) cc_final: 0.7909 (pp20)
REVERT: A  208 VAL cc_start: 0.8977 (t) cc_final: 0.8608 (p)
REVERT: A  272 GLU cc_start: 0.8106 (tt0) cc_final: 0.7738 (tt0)
REVERT: A  369 MET cc_start: 0.9190 (mmm) cc_final: 0.8418 (mmt)
REVERT: A  380 ASP cc_start: 0.8547 (p0) cc_final: 0.8041 (p0)
REVERT: A  512 ASP cc_start: 0.7935 (m-30) cc_final: 0.7665 (p0)
REVERT: A  552 MET cc_start: 0.9421 (mmm) cc_final: 0.8576 (tpp)
REVERT: B   32 MET cc_start: 0.8293 (tpt) cc_final: 0.8022 (tpt)
REVERT: B  127 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8437 (mm-30)
REVERT: B  298 LEU cc_start: 0.9358 (pt) cc_final: 0.9095 (pp)
REVERT: C   30 ARG cc_start: 0.6076 (ttt-90) cc_final: 0.5179 (ttm170)
REVERT: D  117 MET cc_start: 0.9072 (ttp) cc_final: 0.8298 (tmm)
REVERT: D  131 ASP cc_start: 0.8529 (t0) cc_final: 0.8174 (t0)
REVERT: D  178 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8575 (mm-30)
REVERT: D  201 MET cc_start: 0.9139 (mtp) cc_final: 0.8823 (ttm)
REVERT: E   36 ASN cc_start: 0.8223 (t0) cc_final: 0.7925 (t0)
REVERT: E   45 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7345 (mttp)
REVERT: E  105 ASP cc_start: 0.8897 (t0) cc_final: 0.8669 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0980
  time to fit residues: 23.2871
Evaluate side-chains
  117 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 123 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 69 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 131 optimal weight:    0.7980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
A 170 GLN
A 259 ASN
A 371 GLN
A 441 GLN
A 666 ASN
D  40 GLN
E  34 GLN
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.104578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.077603 restraints weight = 29293.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.079954 restraints weight = 17491.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.081547 restraints weight = 12381.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.082651 restraints weight = 9792.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.083315 restraints weight = 8341.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11870  Z= 0.112
  Angle     :  0.538   7.239  16135  Z= 0.285
  Chirality :  0.042   0.147   1765
  Planarity :  0.004   0.050   2123
  Dihedral  :  4.901  22.562   1628
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.69 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.28 (0.21), residues: 1476
  helix:  0.22 (0.30), residues: 292
  sheet: -1.27 (0.25), residues: 411
  loop : -2.41 (0.21), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 120 
 TYR   0.013   0.001   TYR A 578 
 PHE   0.015   0.001   PHE E  74 
 TRP   0.014   0.001   TRP A 776 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (11869)
  covalent geometry    : angle       0.53709 (16133)
  SS BOND              : bond        0.01129 (    1)
  SS BOND              : angle       2.62956 (    2)
  hydrogen bonds       : bond        0.03126 (  429)
  hydrogen bonds       : angle       4.72983 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 171
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5801 (ptt) cc_final: 0.5207 (ptt)
REVERT: A  171 GLU cc_start: 0.8079 (pp20) cc_final: 0.7868 (pp20)
REVERT: A  208 VAL cc_start: 0.8970 (t) cc_final: 0.8602 (p)
REVERT: A  272 GLU cc_start: 0.8116 (tt0) cc_final: 0.7746 (tt0)
REVERT: A  290 ILE cc_start: 0.8834 (pt) cc_final: 0.8566 (mm)
REVERT: A  369 MET cc_start: 0.9181 (mmm) cc_final: 0.8470 (mmt)
REVERT: A  380 ASP cc_start: 0.8530 (p0) cc_final: 0.7961 (p0)
REVERT: A  399 ASP cc_start: 0.8681 (t0) cc_final: 0.8311 (p0)
REVERT: A  445 GLN cc_start: 0.8785 (tp40) cc_final: 0.8476 (tp40)
REVERT: A  512 ASP cc_start: 0.7965 (m-30) cc_final: 0.7689 (p0)
REVERT: A  552 MET cc_start: 0.9469 (mmm) cc_final: 0.8450 (tpp)
REVERT: B   32 MET cc_start: 0.8276 (tpt) cc_final: 0.8012 (tpt)
REVERT: B  370 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8232 (pt0)
REVERT: C   30 ARG cc_start: 0.6196 (ttt-90) cc_final: 0.5174 (ttm170)
REVERT: C   82 ILE cc_start: 0.8574 (pt) cc_final: 0.8326 (mm)
REVERT: D  107 TYR cc_start: 0.8982 (t80) cc_final: 0.8327 (t80)
REVERT: D  117 MET cc_start: 0.9007 (ttp) cc_final: 0.8239 (tmm)
REVERT: D  131 ASP cc_start: 0.8433 (t0) cc_final: 0.7963 (t70)
REVERT: D  178 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8482 (mm-30)
REVERT: D  201 MET cc_start: 0.8983 (mtp) cc_final: 0.8613 (ttm)
REVERT: D  227 MET cc_start: 0.7820 (mtm) cc_final: 0.7040 (ttm)
REVERT: E   36 ASN cc_start: 0.8097 (t0) cc_final: 0.7644 (t0)
REVERT: E   53 GLN cc_start: 0.8507 (pm20) cc_final: 0.8267 (pm20)
  outliers start: 2
  outliers final: 1
  residues processed: 173
  average time/residue: 0.0857
  time to fit residues: 22.1953
Evaluate side-chains
  119 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 116 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0170
   chunk 138 optimal weight:    5.9990
   chunk 95 optimal weight:    7.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A  87 GLN
A 170 GLN
A 371 GLN
A 666 ASN
D  54 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.105279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.078340 restraints weight = 29109.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.080674 restraints weight = 17363.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.082305 restraints weight = 12287.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.083406 restraints weight = 9676.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.084144 restraints weight = 8228.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11870  Z= 0.109
  Angle     :  0.531   8.281  16135  Z= 0.280
  Chirality :  0.043   0.164   1765
  Planarity :  0.004   0.049   2123
  Dihedral  :  4.695  22.147   1628
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.61 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.08 (0.21), residues: 1476
  helix:  0.44 (0.30), residues: 297
  sheet: -1.16 (0.25), residues: 426
  loop : -2.31 (0.21), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 132 
 TYR   0.013   0.001   TYR A 578 
 PHE   0.019   0.001   PHE A 394 
 TRP   0.013   0.001   TRP A 776 
 HIS   0.003   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (11869)
  covalent geometry    : angle       0.53071 (16133)
  SS BOND              : bond        0.00418 (    1)
  SS BOND              : angle       2.42944 (    2)
  hydrogen bonds       : bond        0.03001 (  429)
  hydrogen bonds       : angle       4.60051 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5945 (ptt) cc_final: 0.5385 (ptt)
REVERT: A  208 VAL cc_start: 0.8996 (t) cc_final: 0.8770 (t)
REVERT: A  272 GLU cc_start: 0.8040 (tt0) cc_final: 0.7766 (tt0)
REVERT: A  290 ILE cc_start: 0.8838 (pt) cc_final: 0.8637 (mm)
REVERT: A  369 MET cc_start: 0.9183 (mmm) cc_final: 0.8522 (mmt)
REVERT: A  380 ASP cc_start: 0.8535 (p0) cc_final: 0.7951 (p0)
REVERT: A  399 ASP cc_start: 0.8706 (t0) cc_final: 0.8352 (p0)
REVERT: A  512 ASP cc_start: 0.7986 (m-30) cc_final: 0.7699 (p0)
REVERT: A  552 MET cc_start: 0.9453 (mmm) cc_final: 0.8433 (tpp)
REVERT: B   80 LEU cc_start: 0.8735 (tt) cc_final: 0.8411 (tt)
REVERT: B  303 ASP cc_start: 0.7549 (m-30) cc_final: 0.7075 (m-30)
REVERT: B  370 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8420 (pt0)
REVERT: B  379 LEU cc_start: 0.9468 (pp) cc_final: 0.9259 (pp)
REVERT: B  380 ILE cc_start: 0.9463 (tp) cc_final: 0.9227 (tt)
REVERT: C   30 ARG cc_start: 0.6146 (ttt-90) cc_final: 0.5156 (ttm170)
REVERT: C   82 ILE cc_start: 0.8518 (pt) cc_final: 0.8253 (mm)
REVERT: D  107 TYR cc_start: 0.9060 (t80) cc_final: 0.8648 (t80)
REVERT: D  117 MET cc_start: 0.8993 (ttp) cc_final: 0.8217 (tmm)
REVERT: D  178 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: D  201 MET cc_start: 0.8991 (mtp) cc_final: 0.8631 (ttm)
REVERT: E   36 ASN cc_start: 0.8123 (t0) cc_final: 0.7632 (t0)
REVERT: E   94 THR cc_start: 0.9375 (m) cc_final: 0.8822 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0865
  time to fit residues: 22.4634
Evaluate side-chains
  120 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 30 optimal weight:   10.0000
   chunk 108 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 98 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 144 optimal weight:    2.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
A 666 ASN
B 121 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.103121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.076195 restraints weight = 29189.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.078404 restraints weight = 17949.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.079903 restraints weight = 12914.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.080891 restraints weight = 10357.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.081294 restraints weight = 8948.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11870  Z= 0.193
  Angle     :  0.591   7.693  16135  Z= 0.313
  Chirality :  0.044   0.158   1765
  Planarity :  0.004   0.060   2123
  Dihedral  :  4.925  21.753   1628
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.02 (0.21), residues: 1476
  helix:  0.57 (0.31), residues: 297
  sheet: -1.07 (0.25), residues: 420
  loop : -2.35 (0.21), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 127 
 TYR   0.020   0.002   TYR A 578 
 PHE   0.015   0.002   PHE E  74 
 TRP   0.017   0.002   TRP B  48 
 HIS   0.006   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (11869)
  covalent geometry    : angle       0.59078 (16133)
  SS BOND              : bond        0.00698 (    1)
  SS BOND              : angle       2.32099 (    2)
  hydrogen bonds       : bond        0.03413 (  429)
  hydrogen bonds       : angle       4.72953 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5914 (ptt) cc_final: 0.5703 (ptt)
REVERT: A  142 TYR cc_start: 0.9033 (m-80) cc_final: 0.7872 (m-80)
REVERT: A  272 GLU cc_start: 0.8016 (tt0) cc_final: 0.7601 (tt0)
REVERT: A  369 MET cc_start: 0.9190 (mmm) cc_final: 0.8645 (mmt)
REVERT: A  380 ASP cc_start: 0.8573 (p0) cc_final: 0.8064 (p0)
REVERT: A  399 ASP cc_start: 0.8734 (t0) cc_final: 0.8354 (p0)
REVERT: A  445 GLN cc_start: 0.8772 (tp40) cc_final: 0.8545 (tp40)
REVERT: A  512 ASP cc_start: 0.8033 (m-30) cc_final: 0.7712 (p0)
REVERT: A  552 MET cc_start: 0.9467 (mmm) cc_final: 0.8457 (tpp)
REVERT: B  298 LEU cc_start: 0.9380 (pt) cc_final: 0.9072 (pp)
REVERT: C   30 ARG cc_start: 0.6125 (ttt-90) cc_final: 0.5472 (ttm170)
REVERT: D  117 MET cc_start: 0.9076 (ttp) cc_final: 0.8345 (tmm)
REVERT: D  178 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8497 (mm-30)
REVERT: D  201 MET cc_start: 0.9124 (mtp) cc_final: 0.8730 (ttm)
REVERT: E   36 ASN cc_start: 0.8193 (t0) cc_final: 0.7887 (t0)
REVERT: E   94 THR cc_start: 0.9470 (m) cc_final: 0.8953 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0905
  time to fit residues: 21.8663
Evaluate side-chains
  114 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 33 optimal weight:    0.0670
   chunk 86 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 136 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0370
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
A 666 ASN
B 121 HIS
E  34 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.105003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.078467 restraints weight = 28236.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.080862 restraints weight = 16527.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.082504 restraints weight = 11490.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.083623 restraints weight = 8967.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.084333 restraints weight = 7559.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11870  Z= 0.101
  Angle     :  0.544   7.779  16135  Z= 0.284
  Chirality :  0.043   0.153   1765
  Planarity :  0.004   0.052   2123
  Dihedral  :  4.671  21.854   1628
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.76 (0.21), residues: 1476
  helix:  0.87 (0.31), residues: 297
  sheet: -0.98 (0.25), residues: 425
  loop : -2.18 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 127 
 TYR   0.014   0.001   TYR B 388 
 PHE   0.010   0.001   PHE A 394 
 TRP   0.031   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (11869)
  covalent geometry    : angle       0.54307 (16133)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       2.34594 (    2)
  hydrogen bonds       : bond        0.02956 (  429)
  hydrogen bonds       : angle       4.48288 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5889 (ptt) cc_final: 0.5636 (ptt)
REVERT: A  142 TYR cc_start: 0.8955 (m-80) cc_final: 0.7882 (m-80)
REVERT: A  208 VAL cc_start: 0.8863 (t) cc_final: 0.8610 (p)
REVERT: A  272 GLU cc_start: 0.8015 (tt0) cc_final: 0.7574 (tt0)
REVERT: A  369 MET cc_start: 0.9223 (mmm) cc_final: 0.8633 (mmt)
REVERT: A  380 ASP cc_start: 0.8559 (p0) cc_final: 0.8033 (p0)
REVERT: A  399 ASP cc_start: 0.8727 (t0) cc_final: 0.8330 (p0)
REVERT: A  464 ASP cc_start: 0.7844 (m-30) cc_final: 0.7413 (m-30)
REVERT: A  512 ASP cc_start: 0.8030 (m-30) cc_final: 0.7667 (p0)
REVERT: A  552 MET cc_start: 0.9438 (mmm) cc_final: 0.8411 (tpp)
REVERT: B   32 MET cc_start: 0.8211 (tpt) cc_final: 0.7950 (tpt)
REVERT: B  368 GLN cc_start: 0.7510 (mp10) cc_final: 0.7254 (mp10)
REVERT: B  370 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8328 (pt0)
REVERT: B  379 LEU cc_start: 0.9436 (pp) cc_final: 0.9191 (pp)
REVERT: B  380 ILE cc_start: 0.9364 (tp) cc_final: 0.8998 (tt)
REVERT: C   30 ARG cc_start: 0.6166 (ttt-90) cc_final: 0.5279 (ttm170)
REVERT: C   33 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.7218 (mmm-85)
REVERT: C   82 ILE cc_start: 0.8432 (pt) cc_final: 0.8080 (pt)
REVERT: D  107 TYR cc_start: 0.8983 (t80) cc_final: 0.8499 (t80)
REVERT: D  117 MET cc_start: 0.8995 (ttp) cc_final: 0.8201 (tmm)
REVERT: D  178 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8508 (mm-30)
REVERT: D  218 MET cc_start: 0.8766 (ttt) cc_final: 0.8291 (tmm)
REVERT: E   50 MET cc_start: 0.8642 (tpp) cc_final: 0.7839 (tmm)
REVERT: E   94 THR cc_start: 0.9409 (m) cc_final: 0.8862 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0854
  time to fit residues: 21.6278
Evaluate side-chains
  121 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   chunk 120 optimal weight:    0.7980
   chunk 119 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 122 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 123 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 301 GLN
D 116 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.105740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.078927 restraints weight = 28872.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.081231 restraints weight = 17675.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.082779 restraints weight = 12628.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.083894 restraints weight = 10043.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.084588 restraints weight = 8546.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  11870  Z= 0.118
  Angle     :  0.539   7.925  16135  Z= 0.282
  Chirality :  0.043   0.145   1765
  Planarity :  0.004   0.052   2123
  Dihedral  :  4.577  21.722   1628
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.69 (0.22), residues: 1476
  helix:  0.88 (0.31), residues: 297
  sheet: -0.90 (0.25), residues: 425
  loop : -2.13 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 233 
 TYR   0.015   0.001   TYR B 388 
 PHE   0.011   0.001   PHE A 238 
 TRP   0.020   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (11869)
  covalent geometry    : angle       0.53891 (16133)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       2.19903 (    2)
  hydrogen bonds       : bond        0.02910 (  429)
  hydrogen bonds       : angle       4.44124 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5919 (ptt) cc_final: 0.5652 (ptt)
REVERT: A  142 TYR cc_start: 0.8838 (m-80) cc_final: 0.7891 (m-80)
REVERT: A  272 GLU cc_start: 0.7995 (tt0) cc_final: 0.7580 (tt0)
REVERT: A  369 MET cc_start: 0.9193 (mmm) cc_final: 0.8638 (mmt)
REVERT: A  380 ASP cc_start: 0.8481 (p0) cc_final: 0.7893 (p0)
REVERT: A  399 ASP cc_start: 0.8693 (t0) cc_final: 0.8356 (p0)
REVERT: A  445 GLN cc_start: 0.8743 (tp40) cc_final: 0.8475 (tp40)
REVERT: A  464 ASP cc_start: 0.7830 (m-30) cc_final: 0.7529 (m-30)
REVERT: A  512 ASP cc_start: 0.7948 (m-30) cc_final: 0.7713 (p0)
REVERT: A  552 MET cc_start: 0.9434 (mmm) cc_final: 0.8547 (tpp)
REVERT: A  563 ASN cc_start: 0.8486 (p0) cc_final: 0.8194 (p0)
REVERT: B   32 MET cc_start: 0.8279 (tpt) cc_final: 0.8026 (tpt)
REVERT: B   80 LEU cc_start: 0.8751 (tt) cc_final: 0.8512 (tt)
REVERT: B  298 LEU cc_start: 0.9390 (pt) cc_final: 0.9091 (pp)
REVERT: B  379 LEU cc_start: 0.9461 (pp) cc_final: 0.9214 (pp)
REVERT: B  380 ILE cc_start: 0.9422 (tp) cc_final: 0.9073 (tt)
REVERT: C   30 ARG cc_start: 0.6099 (ttt-90) cc_final: 0.5279 (ttm170)
REVERT: D  107 TYR cc_start: 0.9056 (t80) cc_final: 0.8589 (t80)
REVERT: D  117 MET cc_start: 0.9089 (ttp) cc_final: 0.8337 (tmm)
REVERT: E   36 ASN cc_start: 0.8044 (t0) cc_final: 0.7725 (t0)
REVERT: E   94 THR cc_start: 0.9418 (m) cc_final: 0.8884 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0851
  time to fit residues: 21.1561
Evaluate side-chains
  118 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 144 optimal weight:    0.9980
   chunk 104 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
D 116 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.103796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.077087 restraints weight = 28918.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.079302 restraints weight = 17761.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.080826 restraints weight = 12772.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.081908 restraints weight = 10182.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.082540 restraints weight = 8684.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11870  Z= 0.159
  Angle     :  0.566   7.305  16135  Z= 0.297
  Chirality :  0.043   0.163   1765
  Planarity :  0.004   0.052   2123
  Dihedral  :  4.638  21.467   1628
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.62 (0.22), residues: 1476
  helix:  0.93 (0.31), residues: 302
  sheet: -0.93 (0.25), residues: 427
  loop : -2.06 (0.21), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  47 
 TYR   0.016   0.001   TYR A 578 
 PHE   0.020   0.001   PHE A 394 
 TRP   0.018   0.001   TRP A 546 
 HIS   0.004   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (11869)
  covalent geometry    : angle       0.56506 (16133)
  SS BOND              : bond        0.00203 (    1)
  SS BOND              : angle       2.11658 (    2)
  hydrogen bonds       : bond        0.03125 (  429)
  hydrogen bonds       : angle       4.51838 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5856 (ptt) cc_final: 0.5597 (ptt)
REVERT: A  142 TYR cc_start: 0.8859 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  272 GLU cc_start: 0.7966 (tt0) cc_final: 0.7527 (tt0)
REVERT: A  369 MET cc_start: 0.9197 (mmm) cc_final: 0.8716 (mmt)
REVERT: A  380 ASP cc_start: 0.8534 (p0) cc_final: 0.8026 (p0)
REVERT: A  399 ASP cc_start: 0.8623 (t0) cc_final: 0.8341 (p0)
REVERT: A  464 ASP cc_start: 0.7829 (m-30) cc_final: 0.7513 (m-30)
REVERT: A  512 ASP cc_start: 0.7977 (m-30) cc_final: 0.7704 (p0)
REVERT: A  552 MET cc_start: 0.9391 (mmm) cc_final: 0.8556 (tpp)
REVERT: B  298 LEU cc_start: 0.9407 (pt) cc_final: 0.9086 (pp)
REVERT: B  303 ASP cc_start: 0.7577 (m-30) cc_final: 0.6916 (m-30)
REVERT: B  379 LEU cc_start: 0.9508 (pp) cc_final: 0.9246 (pp)
REVERT: B  380 ILE cc_start: 0.9445 (tp) cc_final: 0.9167 (tt)
REVERT: C   30 ARG cc_start: 0.5870 (ttt-90) cc_final: 0.5353 (ttm170)
REVERT: C   82 ILE cc_start: 0.8515 (pt) cc_final: 0.8303 (pt)
REVERT: D  107 TYR cc_start: 0.9098 (t80) cc_final: 0.8656 (t80)
REVERT: D  117 MET cc_start: 0.9120 (ttp) cc_final: 0.8297 (tmm)
REVERT: D  178 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: D  225 MET cc_start: 0.8865 (mtt) cc_final: 0.8584 (mtt)
REVERT: E   36 ASN cc_start: 0.8147 (t0) cc_final: 0.7823 (t0)
REVERT: E   50 MET cc_start: 0.8665 (tpp) cc_final: 0.7828 (tmm)
REVERT: E   94 THR cc_start: 0.9460 (m) cc_final: 0.8945 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0868
  time to fit residues: 20.8986
Evaluate side-chains
  118 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 84 optimal weight:    0.4980
   chunk 114 optimal weight:    0.0970
   chunk 130 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 117 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
D 116 ASN
D 230 GLN
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.106956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.079086 restraints weight = 28327.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.081547 restraints weight = 16913.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.083233 restraints weight = 11927.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.084391 restraints weight = 9389.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.084993 restraints weight = 7997.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11870  Z= 0.106
  Angle     :  0.557  10.321  16135  Z= 0.290
  Chirality :  0.043   0.173   1765
  Planarity :  0.004   0.090   2123
  Dihedral  :  4.523  21.481   1628
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.42 (0.22), residues: 1476
  helix:  1.13 (0.31), residues: 296
  sheet: -0.81 (0.25), residues: 429
  loop : -1.92 (0.22), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG A  91 
 TYR   0.018   0.001   TYR B 333 
 PHE   0.012   0.001   PHE A 394 
 TRP   0.016   0.001   TRP B  48 
 HIS   0.003   0.001   HIS E  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (11869)
  covalent geometry    : angle       0.55671 (16133)
  SS BOND              : bond        0.00453 (    1)
  SS BOND              : angle       2.53632 (    2)
  hydrogen bonds       : bond        0.02880 (  429)
  hydrogen bonds       : angle       4.41233 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.8860 (m-80) cc_final: 0.7951 (m-80)
REVERT: A  272 GLU cc_start: 0.8082 (tt0) cc_final: 0.7735 (tt0)
REVERT: A  369 MET cc_start: 0.9248 (mmm) cc_final: 0.8729 (mmt)
REVERT: A  380 ASP cc_start: 0.8560 (p0) cc_final: 0.8008 (p0)
REVERT: A  399 ASP cc_start: 0.8670 (t0) cc_final: 0.8332 (p0)
REVERT: A  445 GLN cc_start: 0.8726 (tp40) cc_final: 0.8486 (tp40)
REVERT: A  464 ASP cc_start: 0.7895 (m-30) cc_final: 0.7530 (m-30)
REVERT: A  500 ASP cc_start: 0.8722 (t70) cc_final: 0.8427 (t0)
REVERT: A  512 ASP cc_start: 0.7994 (m-30) cc_final: 0.7693 (p0)
REVERT: A  552 MET cc_start: 0.9428 (mmm) cc_final: 0.8530 (tpp)
REVERT: A  665 CYS cc_start: 0.5882 (t) cc_final: 0.5590 (t)
REVERT: B   32 MET cc_start: 0.8283 (tpt) cc_final: 0.7985 (tpt)
REVERT: B   80 LEU cc_start: 0.8719 (tt) cc_final: 0.8479 (tt)
REVERT: B  298 LEU cc_start: 0.9419 (pt) cc_final: 0.9087 (pp)
REVERT: B  303 ASP cc_start: 0.7614 (m-30) cc_final: 0.6906 (m-30)
REVERT: B  380 ILE cc_start: 0.9401 (tp) cc_final: 0.9126 (tt)
REVERT: C   30 ARG cc_start: 0.5957 (ttt-90) cc_final: 0.5651 (ttm170)
REVERT: C   82 ILE cc_start: 0.8311 (pt) cc_final: 0.8034 (pt)
REVERT: D  107 TYR cc_start: 0.9021 (t80) cc_final: 0.8619 (t80)
REVERT: D  117 MET cc_start: 0.9086 (ttp) cc_final: 0.8334 (tmm)
REVERT: D  178 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7976 (mm-30)
REVERT: D  199 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8164 (tm-30)
REVERT: E   36 ASN cc_start: 0.8057 (t0) cc_final: 0.7686 (t0)
REVERT: E   50 MET cc_start: 0.8695 (tpp) cc_final: 0.7920 (tmm)
REVERT: E   94 THR cc_start: 0.9429 (m) cc_final: 0.8893 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0877
  time to fit residues: 21.8502
Evaluate side-chains
  120 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0050
   chunk 36 optimal weight:    0.0470
   chunk 76 optimal weight:    0.0670
   chunk 136 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.8234

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
D 116 ASN
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.104850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.078592 restraints weight = 28535.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.081028 restraints weight = 16619.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.082722 restraints weight = 11513.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.083835 restraints weight = 8916.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.084587 restraints weight = 7498.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11870  Z= 0.121
  Angle     :  0.564   9.997  16135  Z= 0.293
  Chirality :  0.043   0.172   1765
  Planarity :  0.004   0.052   2123
  Dihedral  :  4.480  21.438   1628
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.36 (0.22), residues: 1476
  helix:  1.14 (0.31), residues: 296
  sheet: -0.71 (0.25), residues: 422
  loop : -1.89 (0.22), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  91 
 TYR   0.018   0.001   TYR B 333 
 PHE   0.022   0.001   PHE D 144 
 TRP   0.013   0.001   TRP A 776 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11869)
  covalent geometry    : angle       0.56328 (16133)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       2.33722 (    2)
  hydrogen bonds       : bond        0.02984 (  429)
  hydrogen bonds       : angle       4.42911 ( 1197)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.6105 (ptt) cc_final: 0.5821 (ptt)
REVERT: A  142 TYR cc_start: 0.8840 (m-80) cc_final: 0.7921 (m-80)
REVERT: A  272 GLU cc_start: 0.8007 (tt0) cc_final: 0.7705 (tt0)
REVERT: A  369 MET cc_start: 0.9229 (mmm) cc_final: 0.8761 (mmt)
REVERT: A  380 ASP cc_start: 0.8553 (p0) cc_final: 0.7983 (p0)
REVERT: A  399 ASP cc_start: 0.8628 (t0) cc_final: 0.8343 (p0)
REVERT: A  445 GLN cc_start: 0.8749 (tp40) cc_final: 0.8508 (tp40)
REVERT: A  464 ASP cc_start: 0.7851 (m-30) cc_final: 0.7501 (m-30)
REVERT: A  500 ASP cc_start: 0.8696 (t70) cc_final: 0.8414 (t0)
REVERT: A  512 ASP cc_start: 0.8008 (m-30) cc_final: 0.7730 (p0)
REVERT: A  552 MET cc_start: 0.9406 (mmm) cc_final: 0.8515 (tpp)
REVERT: A  665 CYS cc_start: 0.5882 (t) cc_final: 0.5572 (t)
REVERT: B   32 MET cc_start: 0.8331 (tpt) cc_final: 0.8043 (tpt)
REVERT: B  298 LEU cc_start: 0.9408 (pt) cc_final: 0.9077 (pp)
REVERT: B  303 ASP cc_start: 0.7738 (m-30) cc_final: 0.7045 (m-30)
REVERT: B  368 GLN cc_start: 0.7533 (mp10) cc_final: 0.7276 (mp10)
REVERT: B  380 ILE cc_start: 0.9397 (tp) cc_final: 0.9124 (tt)
REVERT: C   82 ILE cc_start: 0.8366 (pt) cc_final: 0.8103 (pt)
REVERT: D  107 TYR cc_start: 0.9044 (t80) cc_final: 0.8643 (t80)
REVERT: D  117 MET cc_start: 0.9097 (ttp) cc_final: 0.8320 (tmm)
REVERT: D  199 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: D  219 GLU cc_start: 0.8868 (tp30) cc_final: 0.8627 (tp30)
REVERT: E   36 ASN cc_start: 0.8085 (t0) cc_final: 0.7740 (t0)
REVERT: E   50 MET cc_start: 0.8675 (tpp) cc_final: 0.7923 (tmm)
REVERT: E   94 THR cc_start: 0.9436 (m) cc_final: 0.8901 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0847
  time to fit residues: 21.0483
Evaluate side-chains
  122 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0270
   chunk 40 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 91 optimal weight:    0.3980
   chunk 8 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0770
   chunk 81 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
D 116 ASN
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.106578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.079972 restraints weight = 28852.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.082354 restraints weight = 17074.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.084050 restraints weight = 11995.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.085164 restraints weight = 9364.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085894 restraints weight = 7935.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11870  Z= 0.100
  Angle     :  0.551   9.588  16135  Z= 0.286
  Chirality :  0.043   0.164   1765
  Planarity :  0.004   0.053   2123
  Dihedral  :  4.371  21.471   1628
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.27 (0.22), residues: 1476
  helix:  1.16 (0.31), residues: 296
  sheet: -0.62 (0.25), residues: 430
  loop : -1.86 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  47 
 TYR   0.017   0.001   TYR B 333 
 PHE   0.029   0.001   PHE D 144 
 TRP   0.014   0.001   TRP B  48 
 HIS   0.006   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (11869)
  covalent geometry    : angle       0.55112 (16133)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       1.90215 (    2)
  hydrogen bonds       : bond        0.02942 (  429)
  hydrogen bonds       : angle       4.37372 ( 1197)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1743.98 seconds
wall clock time: 30 minutes 57.95 seconds (1857.95 seconds total)