Starting phenix.real_space_refine
on Tue Mar  3 15:01:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w8p_21577/03_2026/6w8p_21577.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w8p_21577/03_2026/6w8p_21577.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w8p_21577/03_2026/6w8p_21577.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w8p_21577/03_2026/6w8p_21577.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w8p_21577/03_2026/6w8p_21577.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w8p_21577/03_2026/6w8p_21577.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 sd=   0.067
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: 5
    Type Number    sf(0)   Gaussians
     K       3      8.98       5
     S      41      5.16       5
     C    4309      2.51       5
     N    1051      2.21       5
     O    1105      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6509
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3216
          Classifications: {'peptide': 418}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 19, 'TRANS': 398}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 39
          Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 3290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3290
          Classifications: {'peptide': 426}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 19, 'TRANS': 406}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 39
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 30
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'  K': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.66, per 1000 atoms: 0.26
  Number of scatterers: 6509
  At special positions: 0
  Unit cell: (98.175, 97.35, 80.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       3     19.00
     S      41     16.00
     O    1105      8.00
     N    1051      7.00
     C    4309      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 196 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 250.5 milliseconds
  

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1612

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      81.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 48
      removed outlier: 3.841A  pdb=" N   SER A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU A  44 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 58
      removed outlier: 3.524A  pdb=" N   THR A  56 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 101
      removed outlier: 4.030A  pdb=" N   ILE A  87 " --> pdb=" O   MET A  83 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   VAL A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA A  91 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 121
    Processing helix  chain 'A' and resid 122 through 133
    Processing helix  chain 'A' and resid 136 through 163
      removed outlier: 4.269A  pdb=" N   ILE A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A 150 " --> pdb=" O   CYS A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 169
      removed outlier: 3.601A  pdb=" N   SER A 169 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 176
    Processing helix  chain 'A' and resid 180 through 202
      removed outlier: 4.007A  pdb=" N   HIS A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   GLY A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      Proline residue:  A 193  - end of helix
    Processing helix  chain 'A' and resid 211 through 224
      removed outlier: 3.663A  pdb=" N   VAL A 215 " --> pdb=" O   TYR A 211 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   VAL A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ILE A 218 " --> pdb=" O   MET A 214 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LEU A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A 220 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
      removed outlier: 3.854A  pdb=" N   SER A 224 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 274
    Processing helix  chain 'A' and resid 276 through 284
      removed outlier: 4.561A  pdb=" N   GLU A 282 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 5.681A  pdb=" N   ARG A 294 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE A 295 " --> pdb=" O   LYS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.839A  pdb=" N   ALA A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 332
    Processing helix  chain 'A' and resid 338 through 363
      removed outlier: 3.657A  pdb=" N   LEU A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
      removed outlier: 3.537A  pdb=" N   SER A 363 " --> pdb=" O   TYR A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 396
      removed outlier: 3.848A  pdb=" N   ARG A 377 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLN A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 435
      removed outlier: 4.833A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
      Proline residue:  A 427  - end of helix
    Processing helix  chain 'A' and resid 436 through 439
    Processing helix  chain 'A' and resid 443 through 470
      removed outlier: 4.396A  pdb=" N   ILE A 447 " --> pdb=" O   PHE A 443 " (cutoff:3.500A)
      Proline residue:  A 456  - end of helix
      removed outlier: 4.891A  pdb=" N   LEU A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   LEU A 461 " --> pdb=" O   CYS A 457 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 50
      removed outlier: 3.903A  pdb=" N   ILE B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 57
      removed outlier: 3.550A  pdb=" N   THR B  56 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 102
    Processing helix  chain 'B' and resid 106 through 122
    Processing helix  chain 'B' and resid 122 through 132
      removed outlier: 3.651A  pdb=" N   THR B 126 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 163
      removed outlier: 4.366A  pdb=" N   ILE B 140 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE B 150 " --> pdb=" O   CYS B 146 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL B 152 " --> pdb=" O   ILE B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 169
    Processing helix  chain 'B' and resid 171 through 176
    Processing helix  chain 'B' and resid 180 through 206
      removed outlier: 3.704A  pdb=" N   GLY B 187 " --> pdb=" O   ARG B 183 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   GLY B 192 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      Proline residue:  B 193  - end of helix
      removed outlier: 3.724A  pdb=" N   LEU B 204 " --> pdb=" O   ALA B 200 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   PHE B 206 " --> pdb=" O   PHE B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 228
      Proline residue:  B 221  - end of helix
      removed outlier: 5.811A  pdb=" N   LYS B 225 " --> pdb=" O   PRO B 221 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   VAL B 226 " --> pdb=" O   TYR B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 283
      removed outlier: 4.423A  pdb=" N   ILE B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASP B 279 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 296
      removed outlier: 6.067A  pdb=" N   ARG B 294 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE B 295 " --> pdb=" O   LYS B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
    Processing helix  chain 'B' and resid 306 through 332
      removed outlier: 3.827A  pdb=" N   ALA B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 363
      removed outlier: 3.608A  pdb=" N   LEU B 347 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
      removed outlier: 3.558A  pdb=" N   SER B 363 " --> pdb=" O   TYR B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 395
      removed outlier: 4.075A  pdb=" N   ARG B 377 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE B 383 " --> pdb=" O   SER B 379 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLN B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 398
      No H-bonds generated for 'chain 'B' and resid 396 through 398'
    Processing helix  chain 'B' and resid 399 through 403
      removed outlier: 4.529A  pdb=" N   ALA B 402 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 435
      removed outlier: 5.144A  pdb=" N   TYR B 426 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
      Proline residue:  B 427  - end of helix
    Processing helix  chain 'B' and resid 436 through 439
    Processing helix  chain 'B' and resid 443 through 455
      removed outlier: 4.313A  pdb=" N   ILE B 447 " --> pdb=" O   PHE B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 470
      removed outlier: 3.626A  pdb=" N   LEU B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1275 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: 0.97

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1995
        1.35 -     1.46: 1633
        1.46 -     1.58: 2978
        1.58 -     1.70: 0
        1.70 -     1.82: 63
  Bond restraints: 6669
  Sorted by residual:
  bond pdb=" CA  PHE A  99 "
       pdb=" C   PHE A  99 "
    ideal  model  delta    sigma   weight residual
    1.522  1.495  0.027 1.37e-02 5.33e+03 3.97e+00
  bond pdb=" N   LEU A 460 "
       pdb=" CA  LEU A 460 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.021 1.25e-02 6.40e+03 2.87e+00
  bond pdb=" CA  SER A 379 "
       pdb=" C   SER A 379 "
    ideal  model  delta    sigma   weight residual
    1.522  1.499  0.023 1.38e-02 5.25e+03 2.78e+00
  bond pdb=" N   PRO A 208 "
       pdb=" CA  PRO A 208 "
    ideal  model  delta    sigma   weight residual
    1.469  1.480 -0.011 7.40e-03 1.83e+04 2.14e+00
  bond pdb=" C   VAL B 272 "
       pdb=" O   VAL B 272 "
    ideal  model  delta    sigma   weight residual
    1.236  1.252 -0.016 1.10e-02 8.26e+03 2.09e+00
  ... (remaining 6664 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 8751
        1.68 -     3.36: 272
        3.36 -     5.03: 65
        5.03 -     6.71: 13
        6.71 -     8.39: 5
  Bond angle restraints: 9106
  Sorted by residual:
  angle pdb=" N   ILE A  87 "
        pdb=" CA  ILE A  87 "
        pdb=" C   ILE A  87 "
      ideal   model   delta    sigma   weight residual
     113.71  108.21    5.50 9.50e-01 1.11e+00 3.36e+01
  angle pdb=" N   ILE A  60 "
        pdb=" CA  ILE A  60 "
        pdb=" C   ILE A  60 "
      ideal   model   delta    sigma   weight residual
     111.77  107.25    4.52 1.04e+00 9.25e-01 1.89e+01
  angle pdb=" N   SER A 408 "
        pdb=" CA  SER A 408 "
        pdb=" C   SER A 408 "
      ideal   model   delta    sigma   weight residual
     114.39  108.96    5.43 1.45e+00 4.76e-01 1.40e+01
  angle pdb=" N   LEU B 355 "
        pdb=" CA  LEU B 355 "
        pdb=" C   LEU B 355 "
      ideal   model   delta    sigma   weight residual
     109.81  117.71   -7.90 2.21e+00 2.05e-01 1.28e+01
  angle pdb=" N   ILE B  60 "
        pdb=" CA  ILE B  60 "
        pdb=" C   ILE B  60 "
      ideal   model   delta    sigma   weight residual
     112.83  109.33    3.50 9.90e-01 1.02e+00 1.25e+01
  ... (remaining 9101 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 3341
       17.55 -    35.11: 391
       35.11 -    52.66: 130
       52.66 -    70.21: 34
       70.21 -    87.76: 9
  Dihedral angle restraints: 3905
    sinusoidal: 1433
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CB  CYS A 144 "
           pdb=" SG  CYS A 144 "
           pdb=" SG  CYS A 196 "
           pdb=" CB  CYS A 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.40  -74.40     1      1.00e+01 1.00e-02 7.02e+01
  dihedral pdb=" CA  VAL A 223 "
           pdb=" C   VAL A 223 "
           pdb=" N   SER A 224 "
           pdb=" CA  SER A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.91   22.09     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  GLN B 406 "
           pdb=" C   GLN B 406 "
           pdb=" N   PRO B 407 "
           pdb=" CA  PRO B 407 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.86  -20.14     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 3902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 687
       0.032 -    0.063: 276
       0.063 -    0.095: 99
       0.095 -    0.126: 49
       0.126 -    0.158: 8
  Chirality restraints: 1119
  Sorted by residual:
  chirality pdb=" CG  LEU A 398 "
            pdb=" CB  LEU A 398 "
            pdb=" CD1 LEU A 398 "
            pdb=" CD2 LEU A 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  TYR A 426 "
            pdb=" N   TYR A 426 "
            pdb=" C   TYR A 426 "
            pdb=" CB  TYR A 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.32e-01
  chirality pdb=" CA  ILE B 150 "
            pdb=" N   ILE B 150 "
            pdb=" C   ILE B 150 "
            pdb=" CB  ILE B 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 1116 not shown)

  Planarity restraints: 1117
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 459 "    0.019 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   PHE A 459 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   PHE A 459 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LEU A 460 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 285 "   -0.032 5.00e-02 4.00e+02   4.82e-02 3.72e+00
        pdb=" N   PRO B 286 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 286 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 286 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 287 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.88e+00
        pdb=" N   PRO A 288 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1114 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.82: 2131
        2.82 -     3.40: 8000
        3.40 -     3.98: 12103
        3.98 -     4.56: 16687
        4.56 -     5.14: 23602
  Nonbonded interactions: 62523
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 200 "
            pdb=" OG  SER A 203 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR B 319 "
            pdb=" OH  TYR B 359 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER A 363 "
            pdb=" OG  SER A 363 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ALA B 200 "
            pdb=" OG  SER B 203 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   GLN A 401 "
            pdb=" NE1 TRP A 410 "
     model   vdw
     2.308 3.120
  ... (remaining 62518 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 33 through 181 or (resid 182 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 183 through 601))
  selection = (chain 'B' and (resid 33 through 173 or (resid 174 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 175 through 228 or resid 250 through 601))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.98
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:             1.080
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.640
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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      :  0.004   0.066   6671  Z= 0.193
  Angle     :  0.759   8.391   9110  Z= 0.432
  Chirality :  0.043   0.158   1119
  Planarity :  0.004   0.048   1117
  Dihedral  : 18.044  87.764   2287
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.41 %
    Favored  : 89.59 %
  Rotamer:
    Outliers : 10.89 %
    Allowed  : 24.93 %
    Favored  : 64.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.25), residues: 836
  helix: -1.70 (0.17), residues: 633
  sheet:  None (None), residues: 0
  loop : -3.79 (0.39), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  35 
 TYR   0.014   0.002   TYR A 313 
 PHE   0.012   0.001   PHE B 351 
 TRP   0.009   0.001   TRP A  92 
 HIS   0.006   0.001   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6669)
  covalent geometry    : angle       0.75855 ( 9106)
  SS BOND              : bond        0.00551 (    2)
  SS BOND              : angle       1.32677 (    4)
  hydrogen bonds       : bond        0.13492 (  438)
  hydrogen bonds       : angle       5.76721 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 161
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A  254 GLU cc_start: 0.7417 (pm20) cc_final: 0.7147 (pm20)
REVERT: A  341 MET cc_start: 0.7426 (tpp) cc_final: 0.7203 (mmm)
REVERT: A  359 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.6994 (t80)
REVERT: A  377 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7976 (mtm-85)
REVERT: B  196 CYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7125 (t)
REVERT: B  415 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8257 (pm20)
  outliers start: 76
  outliers final: 53
  residues processed: 217
  average time/residue: 0.0727
  time to fit residues: 21.6204
Evaluate side-chains
  182 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 125
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   65 GLN
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  222 TYR
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  310 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 184 HIS
B 368 GLN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.178076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.142119 restraints weight = 10350.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.146656 restraints weight = 5071.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.149466 restraints weight = 3477.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.150852 restraints weight = 2847.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.150852 restraints weight = 2571.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6671  Z= 0.169
  Angle     :  0.755   8.704   9110  Z= 0.371
  Chirality :  0.044   0.218   1119
  Planarity :  0.005   0.052   1117
  Dihedral  : 12.063  70.080   1001
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers : 11.60 %
    Allowed  : 28.08 %
    Favored  : 60.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.28), residues: 836
  helix: -0.47 (0.20), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.27 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 174 
 TYR   0.019   0.002   TYR A 313 
 PHE   0.012   0.001   PHE B 351 
 TRP   0.009   0.001   TRP A 410 
 HIS   0.005   0.001   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6669)
  covalent geometry    : angle       0.75140 ( 9106)
  SS BOND              : bond        0.00298 (    2)
  SS BOND              : angle       3.66528 (    4)
  hydrogen bonds       : bond        0.04859 (  438)
  hydrogen bonds       : angle       4.68812 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 145
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8885 (mm)
REVERT: A  254 GLU cc_start: 0.7432 (pm20) cc_final: 0.7078 (pm20)
REVERT: A  341 MET cc_start: 0.7354 (tpp) cc_final: 0.7144 (mmm)
REVERT: A  359 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.6968 (t80)
REVERT: A  377 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7834 (mtm-85)
REVERT: A  415 GLU cc_start: 0.8661 (pm20) cc_final: 0.8105 (pm20)
REVERT: B  196 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7041 (t)
REVERT: B  276 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: B  372 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5168 (mt-10)
REVERT: B  374 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7602 (mm-30)
  outliers start: 81
  outliers final: 57
  residues processed: 203
  average time/residue: 0.0656
  time to fit residues: 18.8418
Evaluate side-chains
  190 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 127
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  222 TYR
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  310 PHE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 80 optimal weight:    7.9990
   chunk 71 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0970
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.183042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.144982 restraints weight = 10325.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.149703 restraints weight = 5082.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.152671 restraints weight = 3498.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.154092 restraints weight = 2868.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.155276 restraints weight = 2597.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6671  Z= 0.160
  Angle     :  0.729   8.547   9110  Z= 0.360
  Chirality :  0.044   0.215   1119
  Planarity :  0.005   0.051   1117
  Dihedral  : 10.964  60.200    977
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers : 11.32 %
    Allowed  : 29.51 %
    Favored  : 59.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.29), residues: 836
  helix: -0.01 (0.20), residues: 612
  sheet:  None (None), residues: 0
  loop : -2.96 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  35 
 TYR   0.018   0.002   TYR B 359 
 PHE   0.012   0.001   PHE B 317 
 TRP   0.007   0.001   TRP A 410 
 HIS   0.004   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6669)
  covalent geometry    : angle       0.72778 ( 9106)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       2.42660 (    4)
  hydrogen bonds       : bond        0.04613 (  438)
  hydrogen bonds       : angle       4.59151 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 140
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8889 (mm)
REVERT: A  206 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6669 (m-10)
REVERT: A  254 GLU cc_start: 0.7423 (pm20) cc_final: 0.7057 (pm20)
REVERT: A  341 MET cc_start: 0.7259 (tpp) cc_final: 0.7040 (mmm)
REVERT: A  359 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7065 (t80)
REVERT: A  377 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8154 (tpp80)
REVERT: A  415 GLU cc_start: 0.8619 (pm20) cc_final: 0.8116 (pm20)
REVERT: B  163 HIS cc_start: 0.8009 (t-90) cc_final: 0.7699 (t-90)
REVERT: B  196 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7057 (t)
REVERT: B  359 TYR cc_start: 0.8807 (m-80) cc_final: 0.8406 (m-80)
REVERT: B  372 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6410 (mt-10)
REVERT: B  374 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7589 (mm-30)
  outliers start: 79
  outliers final: 58
  residues processed: 200
  average time/residue: 0.0650
  time to fit residues: 18.4969
Evaluate side-chains
  192 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 128
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  222 TYR
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 64 optimal weight:    0.0270
   chunk 80 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0970
   chunk 82 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 284 ASN
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.184199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.146912 restraints weight = 10428.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.151671 restraints weight = 5080.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.154665 restraints weight = 3462.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.155995 restraints weight = 2819.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.156651 restraints weight = 2546.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6671  Z= 0.153
  Angle     :  0.718   8.686   9110  Z= 0.353
  Chirality :  0.044   0.205   1119
  Planarity :  0.005   0.056   1117
  Dihedral  : 10.545  60.483    970
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers : 12.61 %
    Allowed  : 29.08 %
    Favored  : 58.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.29), residues: 836
  helix:  0.29 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop : -2.86 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 174 
 TYR   0.032   0.002   TYR B 125 
 PHE   0.011   0.001   PHE B 351 
 TRP   0.008   0.001   TRP B 324 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6669)
  covalent geometry    : angle       0.71645 ( 9106)
  SS BOND              : bond        0.00602 (    2)
  SS BOND              : angle       2.50264 (    4)
  hydrogen bonds       : bond        0.04382 (  438)
  hydrogen bonds       : angle       4.48138 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 135
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 CYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6468 (t)
REVERT: A  206 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6723 (m-10)
REVERT: A  254 GLU cc_start: 0.7452 (pm20) cc_final: 0.7055 (pm20)
REVERT: A  257 SER cc_start: 0.8772 (t) cc_final: 0.8410 (m)
REVERT: A  289 LYS cc_start: 0.9266 (tppt) cc_final: 0.9042 (ttmm)
REVERT: A  341 MET cc_start: 0.7197 (tpp) cc_final: 0.6977 (mmm)
REVERT: A  359 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7187 (t80)
REVERT: A  377 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8092 (tpp80)
REVERT: A  415 GLU cc_start: 0.8622 (pm20) cc_final: 0.8052 (pm20)
REVERT: B  196 CYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7048 (t)
REVERT: B  282 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7341 (tm-30)
REVERT: B  374 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7339 (mm-30)
  outliers start: 88
  outliers final: 66
  residues processed: 201
  average time/residue: 0.0578
  time to fit residues: 16.9185
Evaluate side-chains
  199 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 127
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  222 TYR
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  281 CYS
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 25 optimal weight:    0.0030
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:   40.0000
   chunk 20 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 GLN
** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.183648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.145795 restraints weight = 10478.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.150568 restraints weight = 5096.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.153531 restraints weight = 3487.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.154856 restraints weight = 2846.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.156083 restraints weight = 2576.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6671  Z= 0.162
  Angle     :  0.720   8.685   9110  Z= 0.353
  Chirality :  0.043   0.203   1119
  Planarity :  0.005   0.067   1117
  Dihedral  : 10.264  60.723    966
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers : 12.75 %
    Allowed  : 29.80 %
    Favored  : 57.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.30), residues: 836
  helix:  0.41 (0.21), residues: 619
  sheet:  None (None), residues: 0
  loop : -2.74 (0.44), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 174 
 TYR   0.029   0.002   TYR B 125 
 PHE   0.012   0.001   PHE B  85 
 TRP   0.007   0.001   TRP B 324 
 HIS   0.006   0.001   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6669)
  covalent geometry    : angle       0.71789 ( 9106)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       2.48900 (    4)
  hydrogen bonds       : bond        0.04380 (  438)
  hydrogen bonds       : angle       4.45598 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 135
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 CYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6335 (t)
REVERT: A  206 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6579 (m-10)
REVERT: A  254 GLU cc_start: 0.7461 (pm20) cc_final: 0.7097 (pm20)
REVERT: A  257 SER cc_start: 0.8725 (t) cc_final: 0.8242 (m)
REVERT: A  341 MET cc_start: 0.7290 (tpp) cc_final: 0.7065 (mmm)
REVERT: A  359 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7224 (t80)
REVERT: A  377 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8066 (tpp80)
REVERT: A  393 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8536 (ttm)
REVERT: A  415 GLU cc_start: 0.8601 (pm20) cc_final: 0.8070 (pm20)
REVERT: B  374 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7469 (mm-30)
  outliers start: 89
  outliers final: 70
  residues processed: 198
  average time/residue: 0.0578
  time to fit residues: 16.8245
Evaluate side-chains
  207 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 131
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  222 TYR
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 78 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0770
   chunk 70 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0670
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
A 284 ASN
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 449 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.186318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.148488 restraints weight = 10497.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.153443 restraints weight = 5041.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.156551 restraints weight = 3407.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.158071 restraints weight = 2760.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.159249 restraints weight = 2480.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6671  Z= 0.150
  Angle     :  0.727   8.843   9110  Z= 0.352
  Chirality :  0.043   0.229   1119
  Planarity :  0.004   0.055   1117
  Dihedral  : 10.025  62.185    962
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers : 11.46 %
    Allowed  : 32.09 %
    Favored  : 56.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.30), residues: 836
  helix:  0.53 (0.21), residues: 619
  sheet:  None (None), residues: 0
  loop : -2.64 (0.45), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 174 
 TYR   0.029   0.002   TYR B 125 
 PHE   0.012   0.001   PHE B  85 
 TRP   0.007   0.001   TRP B 324 
 HIS   0.006   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6669)
  covalent geometry    : angle       0.72440 ( 9106)
  SS BOND              : bond        0.00565 (    2)
  SS BOND              : angle       2.80999 (    4)
  hydrogen bonds       : bond        0.04207 (  438)
  hydrogen bonds       : angle       4.38769 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 137
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 CYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6352 (t)
REVERT: A  206 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6593 (m-10)
REVERT: A  254 GLU cc_start: 0.7466 (pm20) cc_final: 0.7113 (pm20)
REVERT: A  289 LYS cc_start: 0.9281 (tppt) cc_final: 0.9022 (ttmm)
REVERT: A  341 MET cc_start: 0.7271 (tpp) cc_final: 0.7049 (mmm)
REVERT: A  359 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7403 (t80)
REVERT: A  377 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8012 (tpp80)
REVERT: A  393 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8561 (ttm)
REVERT: A  415 GLU cc_start: 0.8575 (pm20) cc_final: 0.8064 (pm20)
REVERT: B  372 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6314 (mt-10)
REVERT: B  374 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7197 (mm-30)
  outliers start: 80
  outliers final: 61
  residues processed: 198
  average time/residue: 0.0571
  time to fit residues: 16.5592
Evaluate side-chains
  192 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 125
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  310 PHE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Chi-restraints excluded: chain B residue  450 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.185748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.147276 restraints weight = 10390.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.152287 restraints weight = 5104.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.155315 restraints weight = 3463.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.156605 restraints weight = 2827.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.158053 restraints weight = 2562.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6671  Z= 0.153
  Angle     :  0.732   8.935   9110  Z= 0.357
  Chirality :  0.043   0.229   1119
  Planarity :  0.005   0.056   1117
  Dihedral  :  9.752  62.104    953
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers : 11.75 %
    Allowed  : 31.66 %
    Favored  : 56.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.30), residues: 836
  helix:  0.56 (0.21), residues: 625
  sheet:  None (None), residues: 0
  loop : -2.60 (0.46), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 174 
 TYR   0.024   0.002   TYR B 125 
 PHE   0.012   0.001   PHE B  85 
 TRP   0.007   0.001   TRP B 324 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6669)
  covalent geometry    : angle       0.72932 ( 9106)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       3.15704 (    4)
  hydrogen bonds       : bond        0.04197 (  438)
  hydrogen bonds       : angle       4.38420 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 132
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8763 (mm)
REVERT: A  196 CYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6332 (t)
REVERT: A  206 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6469 (m-10)
REVERT: A  254 GLU cc_start: 0.7475 (pm20) cc_final: 0.7103 (pm20)
REVERT: A  282 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7543 (tm-30)
REVERT: A  289 LYS cc_start: 0.9275 (tppt) cc_final: 0.9012 (ttmm)
REVERT: A  359 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7444 (t80)
REVERT: A  377 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7981 (tpp80)
REVERT: A  393 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8542 (ttm)
REVERT: A  415 GLU cc_start: 0.8559 (pm20) cc_final: 0.8050 (pm20)
REVERT: B  284 ASN cc_start: 0.7649 (m-40) cc_final: 0.7389 (m-40)
REVERT: B  372 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6232 (mt-10)
REVERT: B  374 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7143 (mm-30)
  outliers start: 82
  outliers final: 62
  residues processed: 193
  average time/residue: 0.0560
  time to fit residues: 16.0564
Evaluate side-chains
  199 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 129
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  310 PHE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  359 TYR
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  390 GLN
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Chi-restraints excluded: chain B residue  462 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0470
   chunk 44 optimal weight:    0.0170
   chunk 45 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0070
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.2934

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

Flipped N/Q/H residues before XYZ refinement:
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.190008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.150620 restraints weight = 10707.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.155704 restraints weight = 5288.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.158942 restraints weight = 3633.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.160480 restraints weight = 2969.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.161625 restraints weight = 2683.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6671  Z= 0.147
  Angle     :  0.731   8.882   9110  Z= 0.356
  Chirality :  0.043   0.255   1119
  Planarity :  0.004   0.048   1117
  Dihedral  :  9.428  58.203    951
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers : 10.03 %
    Allowed  : 33.24 %
    Favored  : 56.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.30), residues: 836
  helix:  0.65 (0.21), residues: 623
  sheet:  None (None), residues: 0
  loop : -2.55 (0.46), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 174 
 TYR   0.022   0.002   TYR B 125 
 PHE   0.033   0.001   PHE B 197 
 TRP   0.006   0.001   TRP B 324 
 HIS   0.006   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6669)
  covalent geometry    : angle       0.72865 ( 9106)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       2.77060 (    4)
  hydrogen bonds       : bond        0.04052 (  438)
  hydrogen bonds       : angle       4.34034 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 132
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8696 (mm)
REVERT: A  196 CYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6274 (t)
REVERT: A  206 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6474 (m-10)
REVERT: A  214 MET cc_start: 0.7256 (tmm) cc_final: 0.7052 (tmm)
REVERT: A  254 GLU cc_start: 0.7508 (pm20) cc_final: 0.7137 (pm20)
REVERT: A  282 GLU cc_start: 0.7863 (pp20) cc_final: 0.7547 (tm-30)
REVERT: A  359 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7635 (t80)
REVERT: A  377 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7965 (tpp80)
REVERT: A  393 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8441 (ttm)
REVERT: A  415 GLU cc_start: 0.8536 (pm20) cc_final: 0.8006 (pm20)
REVERT: B  372 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6080 (mt-10)
REVERT: B  374 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7206 (tp30)
REVERT: B  415 GLU cc_start: 0.8635 (pt0) cc_final: 0.8397 (pt0)
  outliers start: 70
  outliers final: 55
  residues processed: 185
  average time/residue: 0.0598
  time to fit residues: 16.3479
Evaluate side-chains
  186 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 124
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  310 PHE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  359 TYR
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  390 GLN
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.188758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.149096 restraints weight = 10784.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.154090 restraints weight = 5355.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.157254 restraints weight = 3687.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.158645 restraints weight = 3017.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.160044 restraints weight = 2731.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6671  Z= 0.161
  Angle     :  0.763  10.227   9110  Z= 0.373
  Chirality :  0.044   0.261   1119
  Planarity :  0.005   0.073   1117
  Dihedral  :  9.223  58.026    947
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  9.74 %
    Allowed  : 33.09 %
    Favored  : 57.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.30), residues: 836
  helix:  0.67 (0.21), residues: 623
  sheet:  None (None), residues: 0
  loop : -2.51 (0.46), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 174 
 TYR   0.026   0.002   TYR B 125 
 PHE   0.025   0.001   PHE B 197 
 TRP   0.011   0.001   TRP B  92 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6669)
  covalent geometry    : angle       0.76059 ( 9106)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       2.73435 (    4)
  hydrogen bonds       : bond        0.04152 (  438)
  hydrogen bonds       : angle       4.34822 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 127
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8706 (mm)
REVERT: A  196 CYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6301 (t)
REVERT: A  206 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6422 (m-10)
REVERT: A  252 LEU cc_start: 0.7467 (tt) cc_final: 0.7023 (mm)
REVERT: A  254 GLU cc_start: 0.7547 (pm20) cc_final: 0.7195 (pm20)
REVERT: A  282 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7554 (tm-30)
REVERT: A  289 LYS cc_start: 0.9331 (mmmt) cc_final: 0.9123 (ttmm)
REVERT: A  359 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7643 (t80)
REVERT: A  377 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7955 (tpp80)
REVERT: A  415 GLU cc_start: 0.8566 (pm20) cc_final: 0.8060 (pm20)
REVERT: B  374 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7227 (tp30)
REVERT: B  415 GLU cc_start: 0.8687 (pt0) cc_final: 0.8456 (pt0)
  outliers start: 68
  outliers final: 54
  residues processed: 180
  average time/residue: 0.0588
  time to fit residues: 15.6436
Evaluate side-chains
  187 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 126
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  205 PHE
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  310 PHE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  359 TYR
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  390 GLN
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 61 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    0.2980
   chunk 22 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0770
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0970
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.186990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.151612 restraints weight = 10285.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.156486 restraints weight = 4964.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.159556 restraints weight = 3316.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.161313 restraints weight = 2651.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.162323 restraints weight = 2346.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6671  Z= 0.155
  Angle     :  0.786   9.018   9110  Z= 0.383
  Chirality :  0.044   0.277   1119
  Planarity :  0.005   0.058   1117
  Dihedral  :  9.072  58.003    945
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.45 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  8.74 %
    Allowed  : 34.24 %
    Favored  : 57.02 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.30), residues: 836
  helix:  0.69 (0.21), residues: 623
  sheet:  None (None), residues: 0
  loop : -2.47 (0.47), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 174 
 TYR   0.024   0.002   TYR B 125 
 PHE   0.026   0.001   PHE B 197 
 TRP   0.010   0.001   TRP B  92 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6669)
  covalent geometry    : angle       0.78334 ( 9106)
  SS BOND              : bond        0.00304 (    2)
  SS BOND              : angle       3.13976 (    4)
  hydrogen bonds       : bond        0.04124 (  438)
  hydrogen bonds       : angle       4.34073 ( 1275)

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 132
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8705 (mm)
REVERT: A  196 CYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6224 (t)
REVERT: A  206 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.6281 (m-10)
REVERT: A  252 LEU cc_start: 0.7380 (tt) cc_final: 0.6988 (mm)
REVERT: A  254 GLU cc_start: 0.7521 (pm20) cc_final: 0.7178 (pm20)
REVERT: A  282 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7545 (tm-30)
REVERT: A  289 LYS cc_start: 0.9287 (mmmt) cc_final: 0.9086 (ttmm)
REVERT: A  359 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: A  377 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7927 (tpp80)
REVERT: A  415 GLU cc_start: 0.8478 (pm20) cc_final: 0.7866 (pm20)
REVERT: B  374 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7150 (mm-30)
  outliers start: 61
  outliers final: 53
  residues processed: 179
  average time/residue: 0.0588
  time to fit residues: 15.6400
Evaluate side-chains
  182 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 122
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 SER
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  359 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  449 HIS
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  310 PHE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  359 TYR
Chi-restraints excluded: chain B residue  374 GLU
Chi-restraints excluded: chain B residue  390 GLN
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  449 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0470
   chunk 6 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0370
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.187086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.151125 restraints weight = 10302.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.155974 restraints weight = 4974.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.159092 restraints weight = 3332.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.160665 restraints weight = 2668.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.161542 restraints weight = 2375.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6671  Z= 0.155
  Angle     :  0.779   9.174   9110  Z= 0.380
  Chirality :  0.044   0.271   1119
  Planarity :  0.005   0.048   1117
  Dihedral  :  8.974  57.934    945
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 34.53 %
    Favored  : 56.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.30), residues: 836
  helix:  0.72 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.42 (0.47), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 174 
 TYR   0.022   0.002   TYR B 125 
 PHE   0.026   0.001   PHE B 197 
 TRP   0.010   0.001   TRP B  92 
 HIS   0.005   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6669)
  covalent geometry    : angle       0.77612 ( 9106)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       3.04855 (    4)
  hydrogen bonds       : bond        0.04101 (  438)
  hydrogen bonds       : angle       4.33281 ( 1275)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1304.38 seconds
wall clock time: 23 minutes 11.11 seconds (1391.11 seconds total)