Starting phenix.real_space_refine
on Tue Jul 29 19:22:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bnq_12232/07_2025/7bnq_12232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bnq_12232/07_2025/7bnq_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_12232/07_2025/7bnq_12232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bnq_12232/07_2025/7bnq_12232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bnq_12232/07_2025/7bnq_12232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bnq_12232/07_2025/7bnq_12232.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.34, per 1000 atoms: 0.63
  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: 2.71
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.34
  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: 3.59

  Time building geometry restraints manager: 3.25 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:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     29.060
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.650
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.83 (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
 TRP   0.022   0.002   TRP A 776 
 HIS   0.005   0.001   HIS B 121 
 PHE   0.019   0.002   PHE A 517 
 TYR   0.024   0.002   TYR A 578 
 ARG   0.004   0.000   ARG A 366 

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

*********************** 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  : 1.215 
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: 0.7619 (tt0)
REVERT: A  380 ASP cc_start: 0.8462 (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: 0.9113 (mm-40) cc_final: 0.8656 (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: 0.2865
  time to fit residues: 78.9790
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  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 133 optimal weight:    0.7980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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  54 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 = 0.3449 r_free = 0.3449 target = 0.103104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.076521 restraints weight = 28414.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.078827 restraints weight = 16675.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.080432 restraints weight = 11755.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11870  Z= 0.165
  Angle     :  0.597   7.776  16135  Z= 0.318
  Chirality :  0.044   0.154   1765
  Planarity :  0.005   0.058   2123
  Dihedral  :  5.315  24.130   1628
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.20), residues: 1476
  helix: -0.77 (0.27), residues: 296
  sheet: -1.56 (0.25), residues: 402
  loop : -2.63 (0.20), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 776 
 HIS   0.005   0.001   HIS A 186 
 PHE   0.013   0.001   PHE A 517 
 TYR   0.020   0.002   TYR A 578 
 ARG   0.008   0.001   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03725 (  429)
  hydrogen bonds       : angle       5.04179 ( 1197)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       1.85212 (    2)
  covalent geometry    : bond        0.00367 (11869)
  covalent geometry    : angle       0.59653 (16133)

*********************** 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: 1
    poor density    : 161
  time to evaluate  : 1.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.5869 (ptt) cc_final: 0.5507 (ptt)
REVERT: A  123 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7394 (mp0)
REVERT: A  139 ASP cc_start: 0.9004 (m-30) cc_final: 0.8760 (m-30)
REVERT: A  142 TYR cc_start: 0.8986 (m-10) cc_final: 0.8065 (m-80)
REVERT: A  171 GLU cc_start: 0.8099 (pp20) cc_final: 0.7898 (pp20)
REVERT: A  208 VAL cc_start: 0.8988 (t) cc_final: 0.8623 (p)
REVERT: A  272 GLU cc_start: 0.8142 (tt0) cc_final: 0.7761 (tt0)
REVERT: A  369 MET cc_start: 0.9198 (mmm) cc_final: 0.8443 (mmt)
REVERT: A  380 ASP cc_start: 0.8601 (p0) cc_final: 0.8090 (p0)
REVERT: A  445 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8815 (tp40)
REVERT: A  512 ASP cc_start: 0.8002 (m-30) cc_final: 0.7753 (p0)
REVERT: A  552 MET cc_start: 0.9436 (mmm) cc_final: 0.8504 (tpp)
REVERT: B   32 MET cc_start: 0.8276 (tpt) cc_final: 0.7994 (tpt)
REVERT: B  127 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8441 (mm-30)
REVERT: B  298 LEU cc_start: 0.9364 (pt) cc_final: 0.9120 (pp)
REVERT: C   30 ARG cc_start: 0.6109 (ttt-90) cc_final: 0.5121 (ttm170)
REVERT: D  117 MET cc_start: 0.9088 (ttp) cc_final: 0.8311 (tmm)
REVERT: D  131 ASP cc_start: 0.8607 (t0) cc_final: 0.8210 (t0)
REVERT: D  178 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: D  201 MET cc_start: 0.9138 (mtp) cc_final: 0.8831 (ttm)
REVERT: E   36 ASN cc_start: 0.8204 (t0) cc_final: 0.7918 (t0)
REVERT: E   45 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7425 (mttp)
REVERT: E  105 ASP cc_start: 0.8913 (t0) cc_final: 0.8690 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2215
  time to fit residues: 52.7514
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  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0170
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 137 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.8026

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.101404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.074456 restraints weight = 29319.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.076639 restraints weight = 18091.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.078149 restraints weight = 13084.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11870  Z= 0.208
  Angle     :  0.604   7.348  16135  Z= 0.321
  Chirality :  0.044   0.138   1765
  Planarity :  0.004   0.049   2123
  Dihedral  :  5.203  22.493   1628
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  5.30 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.21), residues: 1476
  helix: -0.02 (0.30), residues: 302
  sheet: -1.38 (0.25), residues: 400
  loop : -2.52 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 776 
 HIS   0.004   0.001   HIS A 186 
 PHE   0.017   0.002   PHE E  74 
 TYR   0.022   0.002   TYR A 578 
 ARG   0.006   0.001   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  429)
  hydrogen bonds       : angle       4.93144 ( 1197)
  SS BOND              : bond        0.00987 (    1)
  SS BOND              : angle       2.57583 (    2)
  covalent geometry    : bond        0.00462 (11869)
  covalent geometry    : angle       0.60369 (16133)

*********************** 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
  161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ILE cc_start: 0.8894 (pt) cc_final: 0.8673 (mm)
REVERT: A  369 MET cc_start: 0.9178 (mmm) cc_final: 0.8519 (mmt)
REVERT: A  380 ASP cc_start: 0.8607 (p0) cc_final: 0.8141 (p0)
REVERT: A  399 ASP cc_start: 0.8758 (t0) cc_final: 0.8335 (p0)
REVERT: A  512 ASP cc_start: 0.8033 (m-30) cc_final: 0.7756 (p0)
REVERT: A  552 MET cc_start: 0.9448 (mmm) cc_final: 0.8532 (tpp)
REVERT: B  298 LEU cc_start: 0.9349 (pt) cc_final: 0.9060 (pp)
REVERT: B  370 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8459 (pt0)
REVERT: C   30 ARG cc_start: 0.6192 (ttt-90) cc_final: 0.5206 (ttm170)
REVERT: C   33 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.7216 (mmm-85)
REVERT: C   82 ILE cc_start: 0.8648 (pt) cc_final: 0.8424 (pt)
REVERT: D  107 TYR cc_start: 0.9160 (t80) cc_final: 0.8710 (t80)
REVERT: D  117 MET cc_start: 0.9107 (ttp) cc_final: 0.8374 (tmm)
REVERT: D  131 ASP cc_start: 0.8522 (t0) cc_final: 0.8101 (t0)
REVERT: D  178 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8515 (mm-30)
REVERT: D  201 MET cc_start: 0.9141 (mtp) cc_final: 0.8773 (ttm)
REVERT: E   36 ASN cc_start: 0.8249 (t0) cc_final: 0.7806 (t0)
REVERT: E   74 PHE cc_start: 0.8732 (m-10) cc_final: 0.8481 (m-10)
  outliers start: 4
  outliers final: 2
  residues processed: 161
  average time/residue: 0.2146
  time to fit residues: 51.0955
Evaluate side-chains
  119 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 134 optimal weight:    0.0980
   chunk 118 optimal weight:    0.2980
   chunk 127 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 137 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  87 GLN
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
A 666 ASN
E  34 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.104775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.077907 restraints weight = 28949.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.080172 restraints weight = 17610.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.081725 restraints weight = 12588.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11870  Z= 0.108
  Angle     :  0.543   7.322  16135  Z= 0.288
  Chirality :  0.043   0.162   1765
  Planarity :  0.004   0.049   2123
  Dihedral  :  4.917  22.453   1628
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.41 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.21), residues: 1476
  helix:  0.46 (0.31), residues: 297
  sheet: -1.24 (0.25), residues: 421
  loop : -2.36 (0.21), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 776 
 HIS   0.004   0.001   HIS B 121 
 PHE   0.009   0.001   PHE A 238 
 TYR   0.011   0.001   TYR D 205 
 ARG   0.006   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03151 (  429)
  hydrogen bonds       : angle       4.67416 ( 1197)
  SS BOND              : bond        0.00541 (    1)
  SS BOND              : angle       2.27730 (    2)
  covalent geometry    : bond        0.00243 (11869)
  covalent geometry    : angle       0.54198 (16133)

*********************** 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
  171 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 1.346 
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: 0.6246 (ppp) cc_final: 0.5539 (ppp)
REVERT: A  208 VAL cc_start: 0.8999 (t) cc_final: 0.8792 (t)
REVERT: A  369 MET cc_start: 0.9181 (mmm) cc_final: 0.8524 (mmt)
REVERT: A  380 ASP cc_start: 0.8518 (p0) cc_final: 0.8020 (p0)
REVERT: A  399 ASP cc_start: 0.8766 (t0) cc_final: 0.8399 (p0)
REVERT: A  445 GLN cc_start: 0.8844 (tp40) cc_final: 0.8594 (tp40)
REVERT: A  512 ASP cc_start: 0.8008 (m-30) cc_final: 0.7717 (p0)
REVERT: A  552 MET cc_start: 0.9439 (mmm) cc_final: 0.8463 (tpp)
REVERT: B  379 LEU cc_start: 0.9459 (pp) cc_final: 0.9181 (pp)
REVERT: B  380 ILE cc_start: 0.9448 (tp) cc_final: 0.9178 (tt)
REVERT: C   30 ARG cc_start: 0.6200 (ttt-90) cc_final: 0.5196 (ttm170)
REVERT: D  107 TYR cc_start: 0.9057 (t80) cc_final: 0.8619 (t80)
REVERT: D  117 MET cc_start: 0.9006 (ttp) cc_final: 0.8182 (tmm)
REVERT: D  131 ASP cc_start: 0.8484 (t0) cc_final: 0.8125 (t70)
REVERT: D  178 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8521 (mm-30)
REVERT: D  201 MET cc_start: 0.9019 (mtp) cc_final: 0.8647 (ttm)
REVERT: E   36 ASN cc_start: 0.8136 (t0) cc_final: 0.7699 (t0)
REVERT: E   74 PHE cc_start: 0.8743 (m-10) cc_final: 0.8540 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2040
  time to fit residues: 52.7209
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  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 113 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 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 = 0.3460 r_free = 0.3460 target = 0.103498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.076571 restraints weight = 28912.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.078843 restraints weight = 17437.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.080390 restraints weight = 12432.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  11870  Z= 0.162
  Angle     :  0.569   9.880  16135  Z= 0.299
  Chirality :  0.043   0.154   1765
  Planarity :  0.004   0.049   2123
  Dihedral  :  4.897  22.200   1628
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.21), residues: 1476
  helix:  0.66 (0.31), residues: 297
  sheet: -1.20 (0.25), residues: 422
  loop : -2.31 (0.21), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.012   0.001   PHE A 238 
 TYR   0.017   0.002   TYR A 578 
 ARG   0.007   0.000   ARG D 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03244 (  429)
  hydrogen bonds       : angle       4.64398 ( 1197)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       2.43293 (    2)
  covalent geometry    : bond        0.00363 (11869)
  covalent geometry    : angle       0.56855 (16133)

*********************** 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
  157 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.9067 (m-80) cc_final: 0.7913 (m-80)
REVERT: A  369 MET cc_start: 0.9193 (mmm) cc_final: 0.8610 (mmt)
REVERT: A  380 ASP cc_start: 0.8595 (p0) cc_final: 0.8095 (p0)
REVERT: A  399 ASP cc_start: 0.8788 (t0) cc_final: 0.8399 (p0)
REVERT: A  512 ASP cc_start: 0.8066 (m-30) cc_final: 0.7714 (p0)
REVERT: A  552 MET cc_start: 0.9480 (mmm) cc_final: 0.8519 (tpp)
REVERT: B   80 LEU cc_start: 0.8802 (tt) cc_final: 0.8512 (tt)
REVERT: B  298 LEU cc_start: 0.9376 (pt) cc_final: 0.9068 (pp)
REVERT: B  379 LEU cc_start: 0.9469 (pp) cc_final: 0.9199 (pp)
REVERT: B  380 ILE cc_start: 0.9434 (tp) cc_final: 0.9221 (tt)
REVERT: C   30 ARG cc_start: 0.6170 (ttt-90) cc_final: 0.5455 (ttm170)
REVERT: D  117 MET cc_start: 0.9058 (ttp) cc_final: 0.8236 (tmm)
REVERT: D  131 ASP cc_start: 0.8437 (t0) cc_final: 0.8128 (t70)
REVERT: D  178 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8540 (mm-30)
REVERT: E   36 ASN cc_start: 0.8201 (t0) cc_final: 0.7692 (t0)
REVERT: E   74 PHE cc_start: 0.8788 (m-10) cc_final: 0.8525 (m-10)
REVERT: E   94 THR cc_start: 0.9477 (m) cc_final: 0.8961 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2096
  time to fit residues: 48.8212
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  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 119 optimal weight:    0.0060
   chunk 74 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0870
   chunk 136 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 104 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.7376

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  87 GLN
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
E  34 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.105063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.078286 restraints weight = 28910.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.080557 restraints weight = 17589.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.082143 restraints weight = 12569.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11870  Z= 0.114
  Angle     :  0.551   9.094  16135  Z= 0.290
  Chirality :  0.043   0.150   1765
  Planarity :  0.004   0.049   2123
  Dihedral  :  4.746  22.277   1628
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.69 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.21), residues: 1476
  helix:  0.75 (0.31), residues: 297
  sheet: -1.05 (0.25), residues: 422
  loop : -2.20 (0.21), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  48 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.020   0.001   PHE A 394 
 TYR   0.015   0.001   TYR B 388 
 ARG   0.005   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03018 (  429)
  hydrogen bonds       : angle       4.54325 ( 1197)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       2.35391 (    2)
  covalent geometry    : bond        0.00258 (11869)
  covalent geometry    : angle       0.54996 (16133)

*********************** 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
  161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.6038 (ppp) cc_final: 0.5437 (ppp)
REVERT: A  142 TYR cc_start: 0.9005 (m-80) cc_final: 0.7877 (m-80)
REVERT: A  208 VAL cc_start: 0.8891 (t) cc_final: 0.8596 (p)
REVERT: A  272 GLU cc_start: 0.7997 (tt0) cc_final: 0.7585 (tt0)
REVERT: A  369 MET cc_start: 0.9252 (mmm) cc_final: 0.8436 (mmt)
REVERT: A  380 ASP cc_start: 0.8542 (p0) cc_final: 0.8021 (p0)
REVERT: A  399 ASP cc_start: 0.8795 (t0) cc_final: 0.8400 (p0)
REVERT: A  445 GLN cc_start: 0.8755 (tp40) cc_final: 0.8527 (tp40)
REVERT: A  512 ASP cc_start: 0.8039 (m-30) cc_final: 0.7698 (p0)
REVERT: A  552 MET cc_start: 0.9466 (mmm) cc_final: 0.8499 (tpp)
REVERT: B   32 MET cc_start: 0.8301 (tpt) cc_final: 0.7988 (tpt)
REVERT: B  298 LEU cc_start: 0.9384 (pt) cc_final: 0.9099 (pp)
REVERT: B  303 ASP cc_start: 0.7647 (m-30) cc_final: 0.7043 (m-30)
REVERT: B  379 LEU cc_start: 0.9471 (pp) cc_final: 0.9216 (pp)
REVERT: C   30 ARG cc_start: 0.6279 (ttt-90) cc_final: 0.5283 (ttm170)
REVERT: C   33 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7275 (mmm-85)
REVERT: C   82 ILE cc_start: 0.8461 (pt) cc_final: 0.8183 (pt)
REVERT: D  107 TYR cc_start: 0.9005 (t80) cc_final: 0.8567 (t80)
REVERT: D  117 MET cc_start: 0.9003 (ttp) cc_final: 0.8187 (tmm)
REVERT: D  131 ASP cc_start: 0.8324 (t0) cc_final: 0.7881 (t70)
REVERT: D  227 MET cc_start: 0.7698 (mtm) cc_final: 0.7488 (ttm)
REVERT: E   34 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8600 (mm110)
REVERT: E   36 ASN cc_start: 0.8048 (t0) cc_final: 0.7714 (t0)
REVERT: E   94 THR cc_start: 0.9436 (m) cc_final: 0.8907 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2192
  time to fit residues: 53.0675
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  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 122 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0040
   chunk 135 optimal weight:    0.6980
   chunk 111 optimal weight:    3.9990
   overall best weight:    1.1398

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
E  54 GLN
E  88 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.103952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.077403 restraints weight = 29284.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.079653 restraints weight = 17895.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.081193 restraints weight = 12782.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11870  Z= 0.147
  Angle     :  0.562   8.285  16135  Z= 0.296
  Chirality :  0.043   0.145   1765
  Planarity :  0.004   0.049   2123
  Dihedral  :  4.726  22.102   1628
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.22), residues: 1476
  helix:  0.82 (0.31), residues: 301
  sheet: -0.97 (0.25), residues: 422
  loop : -2.13 (0.21), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  48 
 HIS   0.003   0.001   HIS B 121 
 PHE   0.015   0.001   PHE A 394 
 TYR   0.017   0.001   TYR D 205 
 ARG   0.005   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03115 (  429)
  hydrogen bonds       : angle       4.55678 ( 1197)
  SS BOND              : bond        0.00450 (    1)
  SS BOND              : angle       2.24379 (    2)
  covalent geometry    : bond        0.00332 (11869)
  covalent geometry    : angle       0.56143 (16133)

*********************** 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
  154 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.9006 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  272 GLU cc_start: 0.8009 (tt0) cc_final: 0.7531 (tt0)
REVERT: A  369 MET cc_start: 0.9206 (mmm) cc_final: 0.8595 (mmt)
REVERT: A  380 ASP cc_start: 0.8595 (p0) cc_final: 0.8054 (p0)
REVERT: A  399 ASP cc_start: 0.8769 (t0) cc_final: 0.8388 (p0)
REVERT: A  445 GLN cc_start: 0.8779 (tp40) cc_final: 0.8525 (tp40)
REVERT: A  512 ASP cc_start: 0.8078 (m-30) cc_final: 0.7696 (p0)
REVERT: A  552 MET cc_start: 0.9470 (mmm) cc_final: 0.8522 (tpp)
REVERT: B   32 MET cc_start: 0.8321 (tpt) cc_final: 0.8004 (tpt)
REVERT: B   80 LEU cc_start: 0.8839 (tt) cc_final: 0.8587 (tt)
REVERT: B  298 LEU cc_start: 0.9388 (pt) cc_final: 0.9066 (pp)
REVERT: B  303 ASP cc_start: 0.7682 (m-30) cc_final: 0.7129 (m-30)
REVERT: B  380 ILE cc_start: 0.9423 (tp) cc_final: 0.9013 (tt)
REVERT: C   30 ARG cc_start: 0.6221 (ttt-90) cc_final: 0.5346 (ttm170)
REVERT: D  107 TYR cc_start: 0.9081 (t80) cc_final: 0.8677 (t80)
REVERT: D  117 MET cc_start: 0.9042 (ttp) cc_final: 0.8246 (tmm)
REVERT: D  131 ASP cc_start: 0.8320 (t0) cc_final: 0.7829 (t70)
REVERT: E   36 ASN cc_start: 0.8141 (t0) cc_final: 0.7692 (t0)
REVERT: E   50 MET cc_start: 0.8740 (tpp) cc_final: 0.7852 (tmm)
REVERT: E   94 THR cc_start: 0.9452 (m) cc_final: 0.8921 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1931
  time to fit residues: 45.2964
Evaluate side-chains
  113 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 134 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 104 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 75 optimal weight:    0.0980
   chunk 87 optimal weight:    0.6980
   chunk 130 optimal weight:    0.0570
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
B 301 GLN
E  34 GLN
E  88 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.105730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.079314 restraints weight = 29015.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.081633 restraints weight = 17503.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.083238 restraints weight = 12407.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11870  Z= 0.101
  Angle     :  0.538   8.318  16135  Z= 0.283
  Chirality :  0.043   0.175   1765
  Planarity :  0.004   0.049   2123
  Dihedral  :  4.557  22.139   1628
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.22), residues: 1476
  helix:  0.95 (0.31), residues: 300
  sheet: -0.88 (0.25), residues: 427
  loop : -2.02 (0.22), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 776 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.013   0.001   PHE A 394 
 TYR   0.013   0.001   TYR D 205 
 ARG   0.006   0.000   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02868 (  429)
  hydrogen bonds       : angle       4.43961 ( 1197)
  SS BOND              : bond        0.00678 (    1)
  SS BOND              : angle       3.02934 (    2)
  covalent geometry    : bond        0.00228 (11869)
  covalent geometry    : angle       0.53732 (16133)

*********************** 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
  163 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.8839 (m-80) cc_final: 0.7758 (m-80)
REVERT: A  272 GLU cc_start: 0.8020 (tt0) cc_final: 0.7696 (tt0)
REVERT: A  369 MET cc_start: 0.9235 (mmm) cc_final: 0.8606 (mmt)
REVERT: A  380 ASP cc_start: 0.8518 (p0) cc_final: 0.7961 (p0)
REVERT: A  399 ASP cc_start: 0.8771 (t0) cc_final: 0.8400 (p0)
REVERT: A  445 GLN cc_start: 0.8727 (tp40) cc_final: 0.8470 (tp40)
REVERT: A  464 ASP cc_start: 0.7859 (m-30) cc_final: 0.7455 (m-30)
REVERT: A  512 ASP cc_start: 0.7988 (m-30) cc_final: 0.7705 (p0)
REVERT: A  552 MET cc_start: 0.9442 (mmm) cc_final: 0.8611 (tpp)
REVERT: B   32 MET cc_start: 0.8349 (tpt) cc_final: 0.8080 (tpt)
REVERT: B  298 LEU cc_start: 0.9396 (pt) cc_final: 0.9084 (pp)
REVERT: B  380 ILE cc_start: 0.9405 (tp) cc_final: 0.9008 (tt)
REVERT: C   30 ARG cc_start: 0.6005 (ttt-90) cc_final: 0.5415 (ttm170)
REVERT: C   82 ILE cc_start: 0.8440 (pt) cc_final: 0.8170 (pt)
REVERT: D  107 TYR cc_start: 0.9033 (t80) cc_final: 0.8586 (t80)
REVERT: D  117 MET cc_start: 0.8989 (ttp) cc_final: 0.8084 (tmm)
REVERT: D  131 ASP cc_start: 0.8298 (t0) cc_final: 0.7806 (t70)
REVERT: D  178 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7992 (mm-30)
REVERT: D  199 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: E   34 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8608 (tp40)
REVERT: E   50 MET cc_start: 0.8742 (tpp) cc_final: 0.7728 (tmm)
REVERT: E   94 THR cc_start: 0.9408 (m) cc_final: 0.8878 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1861
  time to fit residues: 46.3413
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  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 139 optimal weight:    1.9990
   chunk 130 optimal weight:    0.4980
   chunk 53 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 136 optimal weight:    3.9990
   chunk 118 optimal weight:    0.0570
   chunk 134 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 127 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  87 GLN
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
D 116 ASN
D 230 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.106093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.079313 restraints weight = 29224.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.081737 restraints weight = 17436.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.083395 restraints weight = 12276.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2689

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= 0.103
  Angle     :  0.534   8.053  16135  Z= 0.280
  Chirality :  0.043   0.171   1765
  Planarity :  0.004   0.051   2123
  Dihedral  :  4.473  21.871   1628
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.56 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.22), residues: 1476
  helix:  1.01 (0.31), residues: 300
  sheet: -0.87 (0.25), residues: 431
  loop : -1.92 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 546 
 HIS   0.006   0.001   HIS A 186 
 PHE   0.012   0.001   PHE A 394 
 TYR   0.016   0.001   TYR B 333 
 ARG   0.007   0.000   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02834 (  429)
  hydrogen bonds       : angle       4.39222 ( 1197)
  SS BOND              : bond        0.00485 (    1)
  SS BOND              : angle       1.32053 (    2)
  covalent geometry    : bond        0.00235 (11869)
  covalent geometry    : angle       0.53389 (16133)

*********************** 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
  166 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.8872 (m-80) cc_final: 0.7883 (m-80)
REVERT: A  272 GLU cc_start: 0.8040 (tt0) cc_final: 0.7725 (tt0)
REVERT: A  369 MET cc_start: 0.9191 (mmm) cc_final: 0.8543 (mmt)
REVERT: A  380 ASP cc_start: 0.8557 (p0) cc_final: 0.7951 (p0)
REVERT: A  399 ASP cc_start: 0.8742 (t0) cc_final: 0.8391 (p0)
REVERT: A  445 GLN cc_start: 0.8731 (tp40) cc_final: 0.8480 (tp40)
REVERT: A  464 ASP cc_start: 0.7840 (m-30) cc_final: 0.7464 (m-30)
REVERT: A  500 ASP cc_start: 0.8691 (t70) cc_final: 0.8407 (t0)
REVERT: A  512 ASP cc_start: 0.7993 (m-30) cc_final: 0.7747 (p0)
REVERT: A  552 MET cc_start: 0.9436 (mmm) cc_final: 0.8594 (tpp)
REVERT: B   32 MET cc_start: 0.8358 (tpt) cc_final: 0.8082 (tpt)
REVERT: B   80 LEU cc_start: 0.8728 (tt) cc_final: 0.8493 (tt)
REVERT: B  298 LEU cc_start: 0.9389 (pt) cc_final: 0.9070 (pp)
REVERT: B  380 ILE cc_start: 0.9398 (tp) cc_final: 0.9008 (tt)
REVERT: C   30 ARG cc_start: 0.5907 (ttt-90) cc_final: 0.5383 (tpp-160)
REVERT: C   33 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7211 (mmm-85)
REVERT: C   82 ILE cc_start: 0.8424 (pt) cc_final: 0.8145 (pt)
REVERT: D  107 TYR cc_start: 0.9045 (t80) cc_final: 0.8604 (t80)
REVERT: D  117 MET cc_start: 0.9083 (ttp) cc_final: 0.8319 (tmm)
REVERT: D  131 ASP cc_start: 0.8286 (t0) cc_final: 0.7788 (t70)
REVERT: D  178 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8019 (mm-30)
REVERT: D  199 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: E   36 ASN cc_start: 0.8105 (t0) cc_final: 0.7686 (t0)
REVERT: E   74 PHE cc_start: 0.8750 (m-10) cc_final: 0.8414 (m-10)
REVERT: E   94 THR cc_start: 0.9393 (m) cc_final: 0.8876 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 166
  average time/residue: 0.2022
  time to fit residues: 51.2419
Evaluate side-chains
  125 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 101 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 129 optimal weight:    2.9990
   chunk 80 optimal weight:    0.3980
   chunk 48 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
B 121 HIS
D 116 ASN
E  34 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 = 0.3468 r_free = 0.3468 target = 0.104129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.077897 restraints weight = 28470.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.080247 restraints weight = 16710.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.081933 restraints weight = 11677.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11870  Z= 0.129
  Angle     :  0.548   7.639  16135  Z= 0.288
  Chirality :  0.043   0.164   1765
  Planarity :  0.004   0.050   2123
  Dihedral  :  4.521  21.661   1628
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.08 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.22), residues: 1476
  helix:  1.23 (0.32), residues: 294
  sheet: -0.84 (0.25), residues: 436
  loop : -1.84 (0.22), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 776 
 HIS   0.006   0.001   HIS A 186 
 PHE   0.019   0.001   PHE D 144 
 TYR   0.016   0.001   TYR B 333 
 ARG   0.005   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02989 (  429)
  hydrogen bonds       : angle       4.45326 ( 1197)
  SS BOND              : bond        0.00505 (    1)
  SS BOND              : angle       2.35656 (    2)
  covalent geometry    : bond        0.00292 (11869)
  covalent geometry    : angle       0.54790 (16133)

********************** 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: 1
    poor density    : 161
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.6279 (ppp) cc_final: 0.5632 (ppp)
REVERT: A  142 TYR cc_start: 0.8849 (m-80) cc_final: 0.7894 (m-80)
REVERT: A  272 GLU cc_start: 0.8031 (tt0) cc_final: 0.7721 (tt0)
REVERT: A  369 MET cc_start: 0.9199 (mmm) cc_final: 0.8596 (mmt)
REVERT: A  380 ASP cc_start: 0.8600 (p0) cc_final: 0.8075 (p0)
REVERT: A  399 ASP cc_start: 0.8719 (t0) cc_final: 0.8382 (p0)
REVERT: A  445 GLN cc_start: 0.8778 (tp40) cc_final: 0.8493 (tp40)
REVERT: A  464 ASP cc_start: 0.7899 (m-30) cc_final: 0.7479 (m-30)
REVERT: A  500 ASP cc_start: 0.8736 (t70) cc_final: 0.8448 (t0)
REVERT: A  512 ASP cc_start: 0.8037 (m-30) cc_final: 0.7745 (p0)
REVERT: A  552 MET cc_start: 0.9425 (mmm) cc_final: 0.8587 (tpp)
REVERT: B   32 MET cc_start: 0.8325 (tpt) cc_final: 0.8056 (tpt)
REVERT: B  298 LEU cc_start: 0.9404 (pt) cc_final: 0.9059 (pp)
REVERT: B  380 ILE cc_start: 0.9394 (tp) cc_final: 0.8997 (tt)
REVERT: C   30 ARG cc_start: 0.5933 (ttt-90) cc_final: 0.5667 (ttm170)
REVERT: C   82 ILE cc_start: 0.8423 (pt) cc_final: 0.8150 (pt)
REVERT: D  107 TYR cc_start: 0.9064 (t80) cc_final: 0.8633 (t80)
REVERT: D  117 MET cc_start: 0.9085 (ttp) cc_final: 0.8282 (tmm)
REVERT: D  131 ASP cc_start: 0.8349 (t0) cc_final: 0.7848 (t70)
REVERT: D  199 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8117 (tm-30)
REVERT: E   94 THR cc_start: 0.9422 (m) cc_final: 0.8899 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1979
  time to fit residues: 48.1156
Evaluate side-chains
  125 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 125 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 55 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.105075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.078600 restraints weight = 29145.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.080870 restraints weight = 17669.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.082458 restraints weight = 12652.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11870  Z= 0.121
  Angle     :  0.552   7.732  16135  Z= 0.290
  Chirality :  0.043   0.166   1765
  Planarity :  0.004   0.051   2123
  Dihedral  :  4.485  21.591   1628
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.22), residues: 1476
  helix:  1.26 (0.32), residues: 294
  sheet: -0.76 (0.25), residues: 425
  loop : -1.81 (0.22), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 776 
 HIS   0.006   0.001   HIS A 186 
 PHE   0.017   0.001   PHE D 144 
 TYR   0.016   0.001   TYR B 333 
 ARG   0.005   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03038 (  429)
  hydrogen bonds       : angle       4.41752 ( 1197)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       1.22003 (    2)
  covalent geometry    : bond        0.00277 (11869)
  covalent geometry    : angle       0.55162 (16133)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3566.95 seconds
wall clock time: 62 minutes 47.41 seconds (3767.41 seconds total)