Starting phenix.real_space_refine
on Sun May 11 02:11:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8szk_40919/05_2025/8szk_40919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8szk_40919/05_2025/8szk_40919.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8szk_40919/05_2025/8szk_40919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8szk_40919/05_2025/8szk_40919.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8szk_40919/05_2025/8szk_40919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8szk_40919/05_2025/8szk_40919.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4749      2.51       5
     N    1259      2.21       5
     O    1351      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7392
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 748
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 87}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 691
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 81}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1193
          Classifications: {'peptide': 146}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 141}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "G"
      Number of atoms: 1462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1462
          Classifications: {'peptide': 176}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 167}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "D"
      Number of atoms: 3298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3298
          Classifications: {'peptide': 400}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380}
  Time building chain proxies: 4.43, per 1000 atoms: 0.60
  Number of scatterers: 7392
  At special positions: 0
  Unit cell: (75.9, 113.3, 134.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    1351      8.00
     N    1259      7.00
     C    4749      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.58
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1740

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      52.8% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 36
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'B' and resid 33 through 37
    Processing helix  chain 'B' and resid 39 through 47
    Processing helix  chain 'B' and resid 66 through 83
    Processing helix  chain 'B' and resid 100 through 111
    Processing helix  chain 'C' and resid 4 through 11
    Processing helix  chain 'C' and resid 15 through 20
    Processing helix  chain 'C' and resid 36 through 50
    Processing helix  chain 'C' and resid 136 through 149
      removed outlier: 3.650A  pdb=" N   GLN C 140 " --> pdb=" O   ASP C 136 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG C 149 " --> pdb=" O   GLU C 145 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 31
    Processing helix  chain 'G' and resid 99 through 108
      removed outlier: 3.926A  pdb=" N   GLN G 105 " --> pdb=" O   ASP G 101 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 109 through 111
      No H-bonds generated for 'chain 'G' and resid 109 through 111'
    Processing helix  chain 'G' and resid 118 through 126
      removed outlier: 3.561A  pdb=" N   ILE G 124 " --> pdb=" O   ILE G 120 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU G 125 " --> pdb=" O   ARG G 121 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 135 through 139
      removed outlier: 3.655A  pdb=" N   GLY G 138 " --> pdb=" O   TYR G 135 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 144 through 154
      removed outlier: 3.586A  pdb=" N   LEU G 148 " --> pdb=" O   SER G 144 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 165 through 170
      removed outlier: 3.657A  pdb=" N   LEU G 169 " --> pdb=" O   SER G 165 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR G 170 " --> pdb=" O   VAL G 166 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 165 through 170'
    Processing helix  chain 'D' and resid 66 through 78
    Processing helix  chain 'D' and resid 92 through 110
      removed outlier: 3.859A  pdb=" N   ILE D  96 " --> pdb=" O   LYS D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 116 through 118
      No H-bonds generated for 'chain 'D' and resid 116 through 118'
    Processing helix  chain 'D' and resid 119 through 132
      removed outlier: 3.932A  pdb=" N   ASN D 130 " --> pdb=" O   MET D 126 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE D 132 " --> pdb=" O   SER D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 171
      removed outlier: 4.476A  pdb=" N   LEU D 161 " --> pdb=" O   PRO D 157 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL D 162 " --> pdb=" O   HIS D 158 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU D 164 " --> pdb=" O   GLN D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 176 through 184
      removed outlier: 3.847A  pdb=" N   ARG D 182 " --> pdb=" O   SER D 178 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR D 183 " --> pdb=" O   ILE D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 195
      removed outlier: 3.715A  pdb=" N   VAL D 189 " --> pdb=" O   ASP D 185 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN D 191 " --> pdb=" O   LYS D 187 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   GLU D 194 " --> pdb=" O   GLN D 190 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU D 195 " --> pdb=" O   GLN D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 198
      No H-bonds generated for 'chain 'D' and resid 196 through 198'
    Processing helix  chain 'D' and resid 200 through 218
      removed outlier: 3.624A  pdb=" N   ARG D 204 " --> pdb=" O   ASP D 200 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP D 205 " --> pdb=" O   PRO D 201 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE D 206 " --> pdb=" O   ARG D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 238
      removed outlier: 3.535A  pdb=" N   PHE D 236 " --> pdb=" O   ILE D 232 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   TYR D 238 " --> pdb=" O   LEU D 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 258
      removed outlier: 3.700A  pdb=" N   GLU D 251 " --> pdb=" O   ALA D 247 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE D 252 " --> pdb=" O   GLU D 248 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU D 253 " --> pdb=" O   LEU D 249 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER D 255 " --> pdb=" O   GLU D 251 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASN D 258 " --> pdb=" O   GLY D 254 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 275
      removed outlier: 3.776A  pdb=" N   PHE D 271 " --> pdb=" O   GLU D 267 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU D 272 " --> pdb=" O   HIS D 268 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   MET D 273 " --> pdb=" O   LYS D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 282
    Processing helix  chain 'D' and resid 284 through 301
      removed outlier: 4.097A  pdb=" N   PHE D 288 " --> pdb=" O   GLY D 284 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   ALA D 290 " --> pdb=" O   ALA D 286 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   GLN D 291 " --> pdb=" O   LEU D 287 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TYR D 294 " --> pdb=" O   ALA D 290 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   CYS D 295 " --> pdb=" O   GLN D 291 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL D 296 " --> pdb=" O   LEU D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 305
      No H-bonds generated for 'chain 'D' and resid 303 through 305'
    Processing helix  chain 'D' and resid 306 through 317
      removed outlier: 3.754A  pdb=" N   PHE D 317 " --> pdb=" O   GLY D 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 322 through 337
      removed outlier: 3.549A  pdb=" N   GLU D 326 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   MET D 328 " --> pdb=" O   GLN D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 341 through 346
      removed outlier: 3.522A  pdb=" N   LYS D 346 " --> pdb=" O   PRO D 342 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 348 through 360
      removed outlier: 3.506A  pdb=" N   GLN D 355 " --> pdb=" O   PRO D 351 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 364 through 373
      removed outlier: 3.527A  pdb=" N   ALA D 371 " --> pdb=" O   VAL D 367 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 374 through 377
      removed outlier: 3.553A  pdb=" N   ASN D 377 " --> pdb=" O   PHE D 374 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 374 through 377'
    Processing helix  chain 'D' and resid 378 through 387
      removed outlier: 3.675A  pdb=" N   GLU D 386 " --> pdb=" O   SER D 382 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN D 387 " --> pdb=" O   LEU D 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 387 through 402
      Proline residue:  D 393  - end of helix
      removed outlier: 4.543A  pdb=" N   ALA D 397 " --> pdb=" O   PRO D 393 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   SER D 398 " --> pdb=" O   ILE D 394 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS D 401 " --> pdb=" O   ALA D 397 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 405
      No H-bonds generated for 'chain 'D' and resid 403 through 405'
    Processing helix  chain 'D' and resid 408 through 423
      removed outlier: 3.555A  pdb=" N   ASN D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 449
      removed outlier: 3.596A  pdb=" N   PHE D 430 " --> pdb=" O   ASN D 426 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17
      removed outlier: 3.543A  pdb=" N   ILE A  14 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ILE A   7 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   THR A  16 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 32
      removed outlier: 9.586A  pdb=" N   VAL B  60 " --> pdb=" O   TYR B  18 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LYS B  20 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   PHE B  62 " --> pdb=" O   LYS B  20 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   ILE B  22 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 87
      removed outlier: 3.671A  pdb=" N   ASP C 120 " --> pdb=" O   ASP C 115 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLY C 123 " --> pdb=" O   CYS C  25 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   CYS C  25 " --> pdb=" O   GLY C 123 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE C  55 " --> pdb=" O   PHE C  68 " (cutoff:3.500A)
      removed outlier: 21.024A  pdb=" N   TRP G   5 " --> pdb=" O   LYS G  91 " (cutoff:3.500A)
      removed outlier: 18.378A  pdb=" N   LYS G  91 " --> pdb=" O   TRP G   5 " (cutoff:3.500A)
      removed outlier: 14.280A  pdb=" N   VAL G   7 " --> pdb=" O   TRP G  89 " (cutoff:3.500A)
      removed outlier: 11.643A  pdb=" N   TRP G  89 " --> pdb=" O   VAL G   7 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ILE G   9 " --> pdb=" O   ILE G  87 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   ILE G  87 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ARG G  90 " --> pdb=" O   LYS G  63 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LYS G  63 " --> pdb=" O   ARG G  90 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ALA G  62 " --> pdb=" O   PRO G  58 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU G  64 " --> pdb=" O   HIS G  56 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS G  56 " --> pdb=" O   LEU G  64 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE G  66 " --> pdb=" O   GLU G  54 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   GLU G  54 " --> pdb=" O   ILE G  66 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   THR G  68 " --> pdb=" O   SER G  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 85 through 87
      removed outlier: 18.000A  pdb=" N   SER G  95 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
      removed outlier: 10.026A  pdb=" N   GLN G  97 " --> pdb=" O   PRO C 100 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   ILE C 102 " --> pdb=" O   GLN G  97 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ARG G  90 " --> pdb=" O   LYS G  63 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LYS G  63 " --> pdb=" O   ARG G  90 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ALA G  62 " --> pdb=" O   PRO G  58 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU G  64 " --> pdb=" O   HIS G  56 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS G  56 " --> pdb=" O   LEU G  64 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE G  66 " --> pdb=" O   GLU G  54 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   GLU G  54 " --> pdb=" O   ILE G  66 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   THR G  68 " --> pdb=" O   SER G  52 " (cutoff:3.500A)

    333 hydrogen bonds defined for protein.
    957 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        0.93 -     1.10: 1
        1.10 -     1.28: 1228
        1.28 -     1.46: 2424
        1.46 -     1.64: 3860
        1.64 -     1.81: 51
  Bond restraints: 7564
  Sorted by residual:
  bond pdb=" CG  PRO A  39 "
       pdb=" CD  PRO A  39 "
    ideal  model  delta    sigma   weight residual
    1.503  0.926  0.577 3.40e-02 8.65e+02 2.88e+02
  bond pdb=" N   PRO A  39 "
       pdb=" CD  PRO A  39 "
    ideal  model  delta    sigma   weight residual
    1.473  1.580 -0.107 1.40e-02 5.10e+03 5.86e+01
  bond pdb=" N   PRO A  39 "
       pdb=" CA  PRO A  39 "
    ideal  model  delta    sigma   weight residual
    1.473  1.434  0.039 1.32e-02 5.74e+03 8.85e+00
  bond pdb=" CB  VAL C 108 "
       pdb=" CG1 VAL C 108 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.17e+00
  bond pdb=" CB  TRP G   5 "
       pdb=" CG  TRP G   5 "
    ideal  model  delta    sigma   weight residual
    1.498  1.553 -0.055 3.10e-02 1.04e+03 3.12e+00
  ... (remaining 7559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.35: 10177
        5.35 -    10.70: 36
       10.70 -    16.05: 5
       16.05 -    21.40: 1
       21.40 -    26.75: 1
  Bond angle restraints: 10220
  Sorted by residual:
  angle pdb=" N   PRO A  39 "
        pdb=" CD  PRO A  39 "
        pdb=" CG  PRO A  39 "
      ideal   model   delta    sigma   weight residual
     103.20   76.45   26.75 1.50e+00 4.44e-01 3.18e+02
  angle pdb=" CA  PRO A  39 "
        pdb=" N   PRO A  39 "
        pdb=" CD  PRO A  39 "
      ideal   model   delta    sigma   weight residual
     112.00   96.55   15.45 1.40e+00 5.10e-01 1.22e+02
  angle pdb=" CA  PRO A  39 "
        pdb=" CB  PRO A  39 "
        pdb=" CG  PRO A  39 "
      ideal   model   delta    sigma   weight residual
     104.50   84.91   19.59 1.90e+00 2.77e-01 1.06e+02
  angle pdb=" N   PRO A  39 "
        pdb=" CA  PRO A  39 "
        pdb=" C   PRO A  39 "
      ideal   model   delta    sigma   weight residual
     113.47  123.35   -9.88 1.43e+00 4.89e-01 4.78e+01
  angle pdb=" N   PRO A  39 "
        pdb=" CA  PRO A  39 "
        pdb=" CB  PRO A  39 "
      ideal   model   delta    sigma   weight residual
     103.23   97.31    5.92 1.07e+00 8.73e-01 3.06e+01
  ... (remaining 10215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3875
       17.90 -    35.81: 522
       35.81 -    53.71: 147
       53.71 -    71.62: 26
       71.62 -    89.52: 11
  Dihedral angle restraints: 4581
    sinusoidal: 1917
      harmonic: 2664
  Sorted by residual:
  dihedral pdb=" CA  TRP G  70 "
           pdb=" C   TRP G  70 "
           pdb=" N   GLY G  71 "
           pdb=" CA  GLY G  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.54  -33.46     0      5.00e+00 4.00e-02 4.48e+01
  dihedral pdb=" CA  PHE C  17 "
           pdb=" C   PHE C  17 "
           pdb=" N   PHE C  18 "
           pdb=" CA  PHE C  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.17   23.83     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  GLU C  16 "
           pdb=" C   GLU C  16 "
           pdb=" N   PHE C  17 "
           pdb=" CA  PHE C  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.56  -21.44     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4578 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 961
       0.070 -    0.140: 135
       0.140 -    0.211: 12
       0.211 -    0.281: 4
       0.281 -    0.351: 2
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CA  PRO A  39 "
            pdb=" N   PRO A  39 "
            pdb=" C   PRO A  39 "
            pdb=" CB  PRO A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CB  THR A  23 "
            pdb=" CA  THR A  23 "
            pdb=" OG1 THR A  23 "
            pdb=" CG2 THR A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.25    0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" CA  ILE A  14 "
            pdb=" N   ILE A  14 "
            pdb=" C   ILE A  14 "
            pdb=" CB  ILE A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 1111 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  38 "   -0.108 5.00e-02 4.00e+02   1.47e-01 3.47e+01
        pdb=" N   PRO A  39 "    0.254 5.00e-02 4.00e+02
        pdb=" CA  PRO A  39 "   -0.076 5.00e-02 4.00e+02
        pdb=" CD  PRO A  39 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 115 "    0.013 2.00e-02 2.50e+03   2.63e-02 6.93e+00
        pdb=" C   ASP C 115 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ASP C 115 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU C 116 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  15 "    0.216 9.50e-02 1.11e+02   9.67e-02 5.76e+00
        pdb=" NE  ARG G  15 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  15 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  15 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 921
        2.75 -     3.29: 7655
        3.29 -     3.83: 11653
        3.83 -     4.36: 13340
        4.36 -     4.90: 22349
  Nonbonded interactions: 55918
  Sorted by model distance:
  nonbonded pdb=" O   THR A  63 "
            pdb=" OG1 THR A  66 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" NH2 ARG A  37 "
            pdb=" O   PRO A  38 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   SER C  22 "
            pdb=" OG  SER C  22 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ASN D 417 "
            pdb=" OG1 THR D 421 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ASN D 426 "
            pdb=" OD1 ASN D 426 "
     model   vdw
     2.274 3.040
  ... (remaining 55913 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.050
  Process input model:                     19.030
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
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      :  0.008   0.577   7564  Z= 0.282
  Angle     :  1.047  26.754  10220  Z= 0.584
  Chirality :  0.052   0.351   1114
  Planarity :  0.007   0.147   1312
  Dihedral  : 17.881  89.521   2841
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  :  8.00 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 30.27 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.29), residues: 888
  helix:  0.52 (0.28), residues: 374
  sheet:  0.64 (0.60), residues: 81
  loop : -1.43 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP G   5 
 HIS   0.013   0.002   HIS G  73 
 PHE   0.039   0.002   PHE A  79 
 TYR   0.025   0.002   TYR D 437 
 ARG   0.010   0.001   ARG A  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26457 (  318)
  hydrogen bonds       : angle       7.41926 (  957)
  covalent geometry    : bond        0.00792 ( 7564)
  covalent geometry    : angle       1.04668 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 283
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.7753 (tt) cc_final: 0.7430 (mt)
REVERT: C   49 ARG cc_start: 0.7431 (mmm-85) cc_final: 0.6925 (mmm-85)
REVERT: C   83 ARG cc_start: 0.6327 (mpp80) cc_final: 0.5606 (ptp90)
REVERT: C   91 GLU cc_start: 0.6549 (mp0) cc_final: 0.5786 (mp0)
REVERT: C   98 LYS cc_start: 0.7127 (tttm) cc_final: 0.6639 (tttm)
REVERT: C  104 ASN cc_start: 0.8344 (t0) cc_final: 0.8053 (t0)
REVERT: C  145 GLU cc_start: 0.7497 (tp30) cc_final: 0.7181 (tp30)
REVERT: D   68 GLN cc_start: 0.7170 (pt0) cc_final: 0.6961 (tt0)
REVERT: D  118 SER cc_start: 0.7993 (p) cc_final: 0.7769 (t)
REVERT: D  126 MET cc_start: 0.7685 (tpt) cc_final: 0.7429 (tpt)
REVERT: D  127 ILE cc_start: 0.8375 (mm) cc_final: 0.8169 (mt)
REVERT: D  161 LEU cc_start: 0.8251 (mm) cc_final: 0.7901 (mm)
REVERT: D  191 GLN cc_start: 0.8225 (mt0) cc_final: 0.7953 (mt0)
REVERT: D  204 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7630 (mtm110)
REVERT: D  207 LEU cc_start: 0.8968 (tp) cc_final: 0.8720 (tp)
REVERT: D  208 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8113 (ttpt)
REVERT: D  222 ARG cc_start: 0.8438 (mtp180) cc_final: 0.8130 (mtt180)
REVERT: D  258 ASN cc_start: 0.8305 (t0) cc_final: 0.7999 (t0)
REVERT: D  265 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7814 (mtmm)
REVERT: D  283 LYS cc_start: 0.7994 (tptt) cc_final: 0.7777 (tptt)
REVERT: D  285 LEU cc_start: 0.8081 (tt) cc_final: 0.7796 (tp)
REVERT: D  348 ILE cc_start: 0.7566 (pt) cc_final: 0.7227 (pt)
REVERT: D  349 GLU cc_start: 0.6462 (mp0) cc_final: 0.6071 (mp0)
REVERT: D  389 ASP cc_start: 0.7496 (p0) cc_final: 0.7296 (p0)
REVERT: D  398 SER cc_start: 0.8694 (m) cc_final: 0.8148 (t)
REVERT: D  441 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7204 (mmm-85)
  outliers start: 7
  outliers final: 2
  residues processed: 287
  average time/residue: 0.2390
  time to fit residues: 86.0591
Evaluate side-chains
  266 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 264
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain D residue  304 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0060
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.4134

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

Flipped N/Q/H residues before XYZ refinement:
B  27 HIS
C  37 HIS
G  28 HIS
G  43 HIS
G  73 HIS
G 108 HIS
** D  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  73 GLN
D  77 GLN
D 212 HIS
D 228 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.150899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125378 restraints weight = 12421.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.129644 restraints weight = 6802.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.132522 restraints weight = 4430.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7564  Z= 0.163
  Angle     :  0.721   7.889  10220  Z= 0.379
  Chirality :  0.046   0.281   1114
  Planarity :  0.005   0.040   1312
  Dihedral  :  4.852  30.263    981
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.98 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 27.79 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.28), residues: 888
  helix:  0.73 (0.26), residues: 411
  sheet:  0.68 (0.54), residues: 88
  loop : -1.53 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP G   5 
 HIS   0.012   0.002   HIS G  73 
 PHE   0.023   0.002   PHE D 396 
 TYR   0.015   0.002   TYR D 437 
 ARG   0.007   0.001   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05788 (  318)
  hydrogen bonds       : angle       5.26128 (  957)
  covalent geometry    : bond        0.00349 ( 7564)
  covalent geometry    : angle       0.72142 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 264
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7645 (mt)
REVERT: C   54 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7070 (mt-10)
REVERT: C   91 GLU cc_start: 0.6762 (mp0) cc_final: 0.5907 (mp0)
REVERT: C  104 ASN cc_start: 0.8565 (t0) cc_final: 0.8157 (t0)
REVERT: C  126 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5669 (mp0)
REVERT: C  145 GLU cc_start: 0.7810 (tp30) cc_final: 0.7527 (tp30)
REVERT: G   97 GLN cc_start: 0.8455 (mp10) cc_final: 0.7778 (mm-40)
REVERT: D   68 GLN cc_start: 0.7715 (pt0) cc_final: 0.7319 (tt0)
REVERT: D   75 LEU cc_start: 0.8164 (mm) cc_final: 0.7776 (mm)
REVERT: D  107 TYR cc_start: 0.7860 (t80) cc_final: 0.7658 (t80)
REVERT: D  115 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (tp)
REVERT: D  118 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7941 (t)
REVERT: D  126 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7602 (tpt)
REVERT: D  127 ILE cc_start: 0.8156 (mm) cc_final: 0.7924 (mt)
REVERT: D  161 LEU cc_start: 0.8432 (mm) cc_final: 0.8116 (mm)
REVERT: D  171 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6520 (mt-10)
REVERT: D  191 GLN cc_start: 0.8503 (mt0) cc_final: 0.8280 (mt0)
REVERT: D  194 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7334 (mm-30)
REVERT: D  208 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8073 (ttpt)
REVERT: D  209 THR cc_start: 0.8389 (m) cc_final: 0.8162 (t)
REVERT: D  253 LEU cc_start: 0.8042 (mt) cc_final: 0.7659 (mm)
REVERT: D  256 ILE cc_start: 0.7047 (tt) cc_final: 0.6838 (tt)
REVERT: D  258 ASN cc_start: 0.8661 (t0) cc_final: 0.8402 (t0)
REVERT: D  265 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7752 (mtmm)
REVERT: D  274 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6626 (mmtt)
REVERT: D  283 LYS cc_start: 0.8286 (tptt) cc_final: 0.7858 (tptt)
REVERT: D  285 LEU cc_start: 0.8175 (tt) cc_final: 0.7830 (tp)
REVERT: D  335 GLU cc_start: 0.7549 (tp30) cc_final: 0.7229 (tp30)
REVERT: D  344 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7206 (mm-40)
REVERT: D  355 GLN cc_start: 0.8192 (tp40) cc_final: 0.7785 (tp40)
REVERT: D  377 ASN cc_start: 0.8632 (t0) cc_final: 0.8290 (t0)
REVERT: D  385 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6649 (mm-30)
REVERT: D  401 LYS cc_start: 0.8130 (tppt) cc_final: 0.7871 (ttmm)
REVERT: D  408 ASN cc_start: 0.8256 (t0) cc_final: 0.7731 (t0)
REVERT: D  429 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7658 (tt)
REVERT: D  444 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7451 (tm-30)
  outliers start: 42
  outliers final: 16
  residues processed: 287
  average time/residue: 0.2513
  time to fit residues: 90.7807
Evaluate side-chains
  279 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 256
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   32 GLU
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  155 ASP
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  118 SER
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 44 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C  37 HIS
G  83 GLN
G 146 GLN
D 212 HIS
D 387 ASN
D 406 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.147396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.121960 restraints weight = 12558.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.126259 restraints weight = 6854.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.129262 restraints weight = 4445.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7564  Z= 0.159
  Angle     :  0.665   7.534  10220  Z= 0.348
  Chirality :  0.045   0.274   1114
  Planarity :  0.004   0.037   1312
  Dihedral  :  4.545  28.233    978
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.87 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 29.28 %
    Favored  : 65.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.28), residues: 888
  helix:  0.91 (0.26), residues: 413
  sheet:  0.66 (0.60), residues: 72
  loop : -1.64 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP G   5 
 HIS   0.006   0.001   HIS D 406 
 PHE   0.025   0.002   PHE A  15 
 TYR   0.019   0.002   TYR B  79 
 ARG   0.007   0.001   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05120 (  318)
  hydrogen bonds       : angle       4.83211 (  957)
  covalent geometry    : bond        0.00368 ( 7564)
  covalent geometry    : angle       0.66456 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 269
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7651 (mt)
REVERT: C   54 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6825 (mt-10)
REVERT: C   91 GLU cc_start: 0.6849 (mp0) cc_final: 0.5979 (mp0)
REVERT: C  126 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5727 (mp0)
REVERT: C  149 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7842 (mtm180)
REVERT: G    7 VAL cc_start: 0.8707 (t) cc_final: 0.8410 (m)
REVERT: G   41 ARG cc_start: 0.7521 (mmm-85) cc_final: 0.6940 (mmm-85)
REVERT: G   83 GLN cc_start: 0.8389 (mp-120) cc_final: 0.7844 (mp10)
REVERT: G   97 GLN cc_start: 0.8544 (mp10) cc_final: 0.7914 (mm-40)
REVERT: D   68 GLN cc_start: 0.7781 (pt0) cc_final: 0.7396 (tt0)
REVERT: D  107 TYR cc_start: 0.7944 (t80) cc_final: 0.7722 (t80)
REVERT: D  125 LYS cc_start: 0.8176 (mttm) cc_final: 0.7948 (mtmm)
REVERT: D  161 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8125 (mm)
REVERT: D  171 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6479 (mt-10)
REVERT: D  194 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7332 (mm-30)
REVERT: D  200 ASP cc_start: 0.8546 (t0) cc_final: 0.8279 (t0)
REVERT: D  207 LEU cc_start: 0.8262 (tp) cc_final: 0.8058 (mp)
REVERT: D  208 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7667 (ttpt)
REVERT: D  248 GLU cc_start: 0.7390 (mp0) cc_final: 0.6485 (mp0)
REVERT: D  251 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7097 (mt-10)
REVERT: D  256 ILE cc_start: 0.7113 (tt) cc_final: 0.6846 (tt)
REVERT: D  258 ASN cc_start: 0.8608 (t0) cc_final: 0.8361 (t0)
REVERT: D  265 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7845 (mtmm)
REVERT: D  274 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6655 (mmtt)
REVERT: D  283 LYS cc_start: 0.8298 (tptt) cc_final: 0.7840 (tptt)
REVERT: D  285 LEU cc_start: 0.8252 (tt) cc_final: 0.7905 (tp)
REVERT: D  335 GLU cc_start: 0.7572 (tp30) cc_final: 0.7360 (tp30)
REVERT: D  344 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7114 (mm-40)
REVERT: D  347 LYS cc_start: 0.7790 (mttp) cc_final: 0.7248 (mttp)
REVERT: D  355 GLN cc_start: 0.8227 (tp40) cc_final: 0.7783 (tp40)
REVERT: D  373 TYR cc_start: 0.8338 (m-10) cc_final: 0.8098 (m-80)
REVERT: D  377 ASN cc_start: 0.8701 (t0) cc_final: 0.8466 (t0)
REVERT: D  408 ASN cc_start: 0.8439 (t0) cc_final: 0.8220 (t0)
REVERT: D  429 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7526 (tt)
REVERT: D  441 ARG cc_start: 0.7689 (mmm160) cc_final: 0.7411 (mmm160)
  outliers start: 39
  outliers final: 23
  residues processed: 282
  average time/residue: 0.2527
  time to fit residues: 89.2826
Evaluate side-chains
  288 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 260
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  155 ASP
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  394 ILE
Chi-restraints excluded: chain D residue  411 ILE
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    0.0010
   chunk 60 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0870
   chunk 5 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.1768

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

Flipped N/Q/H residues before XYZ refinement:
B  27 HIS
G 105 GLN
G 139 HIS
D 212 HIS
D 387 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.144451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.119333 restraints weight = 12366.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.123615 restraints weight = 6659.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.126574 restraints weight = 4284.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7564  Z= 0.195
  Angle     :  0.669   7.242  10220  Z= 0.351
  Chirality :  0.045   0.194   1114
  Planarity :  0.005   0.080   1312
  Dihedral  :  4.579  27.192    978
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.88 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 28.78 %
    Favored  : 64.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.28), residues: 888
  helix:  0.96 (0.26), residues: 415
  sheet:  0.37 (0.57), residues: 81
  loop : -1.70 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP G   5 
 HIS   0.007   0.001   HIS D 212 
 PHE   0.024   0.002   PHE A  15 
 TYR   0.028   0.002   TYR B  79 
 ARG   0.012   0.001   ARG D 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05004 (  318)
  hydrogen bonds       : angle       4.67425 (  957)
  covalent geometry    : bond        0.00442 ( 7564)
  covalent geometry    : angle       0.66926 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 251
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   24 GLU cc_start: 0.6491 (tp30) cc_final: 0.6252 (tp30)
REVERT: C   91 GLU cc_start: 0.6797 (mp0) cc_final: 0.5906 (mp0)
REVERT: C  113 TRP cc_start: 0.8406 (p-90) cc_final: 0.7714 (p-90)
REVERT: C  122 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6279 (tpp)
REVERT: C  126 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5874 (mp0)
REVERT: C  149 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8161 (mtm180)
REVERT: G    7 VAL cc_start: 0.8714 (t) cc_final: 0.8404 (m)
REVERT: G   41 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7229 (mmm-85)
REVERT: G   70 TRP cc_start: 0.6890 (p90) cc_final: 0.6528 (p90)
REVERT: G   97 GLN cc_start: 0.8577 (mp10) cc_final: 0.7993 (mm-40)
REVERT: G  127 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7291 (mtt180)
REVERT: D   68 GLN cc_start: 0.7815 (pt0) cc_final: 0.7445 (tt0)
REVERT: D   69 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6610 (tm-30)
REVERT: D   77 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8306 (tm-30)
REVERT: D  125 LYS cc_start: 0.8148 (mttm) cc_final: 0.7937 (mtmm)
REVERT: D  161 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8145 (mm)
REVERT: D  171 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6548 (mt-10)
REVERT: D  194 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7361 (mm-30)
REVERT: D  200 ASP cc_start: 0.8554 (t0) cc_final: 0.8310 (t0)
REVERT: D  207 LEU cc_start: 0.8283 (tp) cc_final: 0.8053 (mp)
REVERT: D  208 LYS cc_start: 0.8454 (ttpt) cc_final: 0.7902 (ttpt)
REVERT: D  229 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7077 (mt)
REVERT: D  248 GLU cc_start: 0.7360 (mp0) cc_final: 0.6547 (mp0)
REVERT: D  251 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7088 (mt-10)
REVERT: D  258 ASN cc_start: 0.8520 (t0) cc_final: 0.8212 (t0)
REVERT: D  265 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7833 (mtmm)
REVERT: D  274 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6660 (mmtt)
REVERT: D  283 LYS cc_start: 0.8217 (tptt) cc_final: 0.7811 (tptt)
REVERT: D  285 LEU cc_start: 0.8368 (tt) cc_final: 0.8001 (tp)
REVERT: D  303 ASP cc_start: 0.8001 (t0) cc_final: 0.7651 (t0)
REVERT: D  326 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6599 (tp30)
REVERT: D  335 GLU cc_start: 0.7675 (tp30) cc_final: 0.7257 (tp30)
REVERT: D  344 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7308 (mm-40)
REVERT: D  355 GLN cc_start: 0.8211 (tp40) cc_final: 0.7807 (tp40)
REVERT: D  373 TYR cc_start: 0.8335 (m-10) cc_final: 0.8050 (m-80)
REVERT: D  377 ASN cc_start: 0.8695 (t0) cc_final: 0.8412 (t0)
REVERT: D  396 PHE cc_start: 0.8282 (t80) cc_final: 0.8045 (t80)
REVERT: D  408 ASN cc_start: 0.8479 (t0) cc_final: 0.8226 (t0)
  outliers start: 54
  outliers final: 29
  residues processed: 274
  average time/residue: 0.2472
  time to fit residues: 85.2164
Evaluate side-chains
  285 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 250
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  155 ASP
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain G residue  130 SER
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain D residue  229 ILE
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  394 ILE
Chi-restraints excluded: chain D residue  404 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 86 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0030
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 HIS
** D 289 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 = 0.3915 r_free = 0.3915 target = 0.145042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.119897 restraints weight = 12403.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.124177 restraints weight = 6709.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.127125 restraints weight = 4326.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7564  Z= 0.142
  Angle     :  0.638  10.632  10220  Z= 0.328
  Chirality :  0.044   0.288   1114
  Planarity :  0.004   0.036   1312
  Dihedral  :  4.538  27.080    978
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.21 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 29.03 %
    Favored  : 65.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.28), residues: 888
  helix:  1.16 (0.26), residues: 408
  sheet:  0.59 (0.58), residues: 81
  loop : -1.70 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 375 
 HIS   0.009   0.001   HIS A  10 
 PHE   0.022   0.002   PHE A  79 
 TYR   0.021   0.001   TYR B  79 
 ARG   0.010   0.001   ARG D 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  318)
  hydrogen bonds       : angle       4.51444 (  957)
  covalent geometry    : bond        0.00327 ( 7564)
  covalent geometry    : angle       0.63805 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 246
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4045 (OUTLIER) cc_final: 0.2921 (mmt90)
REVERT: C   24 GLU cc_start: 0.6491 (tp30) cc_final: 0.6221 (tp30)
REVERT: C   49 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7758 (mmm-85)
REVERT: C  113 TRP cc_start: 0.8395 (p-90) cc_final: 0.7714 (p-90)
REVERT: C  122 MET cc_start: 0.6588 (tpt) cc_final: 0.5965 (tpp)
REVERT: C  126 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5916 (mp0)
REVERT: C  149 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.8175 (mtm180)
REVERT: G    7 VAL cc_start: 0.8653 (t) cc_final: 0.8321 (m)
REVERT: G   97 GLN cc_start: 0.8536 (mp10) cc_final: 0.7951 (mm-40)
REVERT: D   68 GLN cc_start: 0.7816 (pt0) cc_final: 0.7450 (tt0)
REVERT: D   69 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6612 (tm-30)
REVERT: D   77 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (tm-30)
REVERT: D  125 LYS cc_start: 0.8169 (mttm) cc_final: 0.7951 (mtmm)
REVERT: D  161 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8126 (mm)
REVERT: D  171 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6549 (mt-10)
REVERT: D  190 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: D  194 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7340 (mm-30)
REVERT: D  200 ASP cc_start: 0.8551 (t0) cc_final: 0.8335 (t0)
REVERT: D  208 LYS cc_start: 0.8483 (ttpt) cc_final: 0.7934 (ttpt)
REVERT: D  234 LEU cc_start: 0.8427 (mt) cc_final: 0.8104 (mt)
REVERT: D  248 GLU cc_start: 0.7377 (mp0) cc_final: 0.6606 (mp0)
REVERT: D  251 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7108 (mt-10)
REVERT: D  258 ASN cc_start: 0.8528 (t0) cc_final: 0.8224 (t0)
REVERT: D  265 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7770 (mtmm)
REVERT: D  274 LYS cc_start: 0.6997 (mmtt) cc_final: 0.6602 (mmtt)
REVERT: D  283 LYS cc_start: 0.8217 (tptt) cc_final: 0.7780 (tptt)
REVERT: D  285 LEU cc_start: 0.8294 (tt) cc_final: 0.7931 (tp)
REVERT: D  320 LYS cc_start: 0.8171 (tppt) cc_final: 0.7399 (tppt)
REVERT: D  326 GLU cc_start: 0.6917 (tt0) cc_final: 0.6539 (tp30)
REVERT: D  335 GLU cc_start: 0.7665 (tp30) cc_final: 0.7254 (tp30)
REVERT: D  344 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7313 (mm-40)
REVERT: D  355 GLN cc_start: 0.8188 (tp40) cc_final: 0.7752 (tp40)
REVERT: D  373 TYR cc_start: 0.8306 (m-10) cc_final: 0.8031 (m-80)
REVERT: D  377 ASN cc_start: 0.8666 (t0) cc_final: 0.8286 (t0)
REVERT: D  396 PHE cc_start: 0.8234 (t80) cc_final: 0.8031 (t80)
REVERT: D  408 ASN cc_start: 0.8518 (t0) cc_final: 0.8216 (t0)
  outliers start: 44
  outliers final: 26
  residues processed: 267
  average time/residue: 0.2306
  time to fit residues: 78.0018
Evaluate side-chains
  271 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 241
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  155 ASP
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain G residue  130 SER
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  394 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0050
   chunk 70 optimal weight:    0.0020
   overall best weight:    0.6006

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 HIS
** D 289 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 = 0.3921 r_free = 0.3921 target = 0.145608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.120720 restraints weight = 12346.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.125012 restraints weight = 6651.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.127944 restraints weight = 4274.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7564  Z= 0.133
  Angle     :  0.650  11.090  10220  Z= 0.327
  Chirality :  0.044   0.316   1114
  Planarity :  0.004   0.046   1312
  Dihedral  :  4.489  26.397    978
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.55 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.40 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.28), residues: 888
  helix:  1.16 (0.26), residues: 407
  sheet:  0.65 (0.58), residues: 81
  loop : -1.69 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 375 
 HIS   0.014   0.001   HIS A  10 
 PHE   0.023   0.002   PHE A  15 
 TYR   0.020   0.001   TYR B  79 
 ARG   0.007   0.001   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04058 (  318)
  hydrogen bonds       : angle       4.43796 (  957)
  covalent geometry    : bond        0.00310 ( 7564)
  covalent geometry    : angle       0.64969 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 245
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4003 (OUTLIER) cc_final: 0.2833 (mmt90)
REVERT: B   60 VAL cc_start: 0.8312 (p) cc_final: 0.8091 (p)
REVERT: C   24 GLU cc_start: 0.6539 (tp30) cc_final: 0.6281 (tp30)
REVERT: C   54 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7084 (mt-10)
REVERT: C  113 TRP cc_start: 0.8392 (p-90) cc_final: 0.7718 (p-90)
REVERT: C  126 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5904 (mp0)
REVERT: C  149 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8217 (mtm180)
REVERT: G    7 VAL cc_start: 0.8583 (t) cc_final: 0.8273 (m)
REVERT: G   97 GLN cc_start: 0.8526 (mp10) cc_final: 0.7932 (mm-40)
REVERT: G  108 HIS cc_start: 0.7869 (t70) cc_final: 0.7613 (t70)
REVERT: G  139 HIS cc_start: 0.6938 (m-70) cc_final: 0.6508 (m90)
REVERT: D   68 GLN cc_start: 0.7814 (pt0) cc_final: 0.7463 (tt0)
REVERT: D   69 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6593 (tm-30)
REVERT: D   77 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8350 (tm-30)
REVERT: D  161 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8158 (mm)
REVERT: D  171 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6454 (mt-10)
REVERT: D  190 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: D  194 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7323 (mm-30)
REVERT: D  200 ASP cc_start: 0.8562 (t0) cc_final: 0.8350 (t0)
REVERT: D  208 LYS cc_start: 0.8481 (ttpt) cc_final: 0.7925 (ttpt)
REVERT: D  234 LEU cc_start: 0.8474 (mt) cc_final: 0.8150 (mt)
REVERT: D  248 GLU cc_start: 0.7375 (mp0) cc_final: 0.6635 (mp0)
REVERT: D  251 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7097 (mt-10)
REVERT: D  258 ASN cc_start: 0.8488 (t0) cc_final: 0.8228 (t0)
REVERT: D  265 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7764 (mtmm)
REVERT: D  274 LYS cc_start: 0.6946 (mmtt) cc_final: 0.6543 (mmtt)
REVERT: D  279 MET cc_start: 0.8417 (tpp) cc_final: 0.7985 (tpp)
REVERT: D  283 LYS cc_start: 0.8184 (tptt) cc_final: 0.7785 (tptt)
REVERT: D  285 LEU cc_start: 0.8298 (tt) cc_final: 0.7955 (tp)
REVERT: D  302 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7410 (mtpp)
REVERT: D  320 LYS cc_start: 0.8174 (tppt) cc_final: 0.7410 (tppt)
REVERT: D  326 GLU cc_start: 0.6886 (tt0) cc_final: 0.6530 (tp30)
REVERT: D  335 GLU cc_start: 0.7639 (tp30) cc_final: 0.7240 (tp30)
REVERT: D  344 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7299 (mm-40)
REVERT: D  355 GLN cc_start: 0.8161 (tp40) cc_final: 0.7741 (tp40)
REVERT: D  373 TYR cc_start: 0.8300 (m-10) cc_final: 0.8037 (m-80)
REVERT: D  377 ASN cc_start: 0.8663 (t0) cc_final: 0.8286 (t0)
REVERT: D  408 ASN cc_start: 0.8498 (t0) cc_final: 0.8226 (t0)
  outliers start: 42
  outliers final: 29
  residues processed: 268
  average time/residue: 0.2317
  time to fit residues: 78.8575
Evaluate side-chains
  275 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 241
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   25 CYS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  155 ASP
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   80 HIS
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain G residue  130 SER
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  394 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 75 optimal weight:    0.3980
   chunk 35 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0060
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 HIS
D 289 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.146034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.121008 restraints weight = 12509.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.125288 restraints weight = 6719.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.128251 restraints weight = 4325.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7564  Z= 0.129
  Angle     :  0.664  11.706  10220  Z= 0.335
  Chirality :  0.044   0.323   1114
  Planarity :  0.005   0.064   1312
  Dihedral  :  4.447  26.566    978
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.09 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 30.27 %
    Favored  : 65.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.28), residues: 888
  helix:  1.20 (0.27), residues: 407
  sheet:  0.62 (0.58), residues: 81
  loop : -1.67 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 375 
 HIS   0.014   0.001   HIS A  10 
 PHE   0.027   0.002   PHE D 396 
 TYR   0.018   0.002   TYR B  79 
 ARG   0.006   0.001   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03845 (  318)
  hydrogen bonds       : angle       4.36379 (  957)
  covalent geometry    : bond        0.00298 ( 7564)
  covalent geometry    : angle       0.66369 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 244
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4258 (OUTLIER) cc_final: 0.3178 (mmt90)
REVERT: B   60 VAL cc_start: 0.8160 (p) cc_final: 0.7937 (p)
REVERT: C   54 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7112 (mt-10)
REVERT: C  113 TRP cc_start: 0.8385 (p-90) cc_final: 0.7716 (p-90)
REVERT: C  122 MET cc_start: 0.6726 (tpt) cc_final: 0.6323 (tpp)
REVERT: C  126 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5915 (mp0)
REVERT: C  149 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8198 (mtm180)
REVERT: G    7 VAL cc_start: 0.8513 (t) cc_final: 0.8207 (m)
REVERT: G   69 TYR cc_start: 0.7702 (m-10) cc_final: 0.7341 (m-80)
REVERT: G  108 HIS cc_start: 0.7891 (t70) cc_final: 0.7656 (t70)
REVERT: G  135 TYR cc_start: 0.7870 (t80) cc_final: 0.7494 (t80)
REVERT: D   68 GLN cc_start: 0.7811 (pt0) cc_final: 0.7489 (tt0)
REVERT: D   77 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8356 (tm-30)
REVERT: D  102 ASN cc_start: 0.8479 (m-40) cc_final: 0.8218 (m-40)
REVERT: D  161 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8161 (mm)
REVERT: D  171 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6451 (mt-10)
REVERT: D  194 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: D  200 ASP cc_start: 0.8559 (t0) cc_final: 0.8332 (t0)
REVERT: D  203 GLU cc_start: 0.8019 (tt0) cc_final: 0.7796 (tt0)
REVERT: D  208 LYS cc_start: 0.8480 (ttpt) cc_final: 0.7920 (ttpt)
REVERT: D  234 LEU cc_start: 0.8441 (mt) cc_final: 0.8064 (mt)
REVERT: D  251 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7074 (mt-10)
REVERT: D  258 ASN cc_start: 0.8445 (t0) cc_final: 0.8214 (t0)
REVERT: D  265 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7771 (mtmm)
REVERT: D  274 LYS cc_start: 0.7007 (mmtt) cc_final: 0.6591 (mmtt)
REVERT: D  279 MET cc_start: 0.8391 (tpp) cc_final: 0.7981 (tpp)
REVERT: D  283 LYS cc_start: 0.8193 (tptt) cc_final: 0.7799 (tptt)
REVERT: D  285 LEU cc_start: 0.8275 (tt) cc_final: 0.7943 (tp)
REVERT: D  302 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7407 (mtpp)
REVERT: D  320 LYS cc_start: 0.8196 (tppt) cc_final: 0.7432 (tppt)
REVERT: D  326 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6546 (tp30)
REVERT: D  335 GLU cc_start: 0.7639 (tp30) cc_final: 0.7262 (tp30)
REVERT: D  344 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7307 (mm-40)
REVERT: D  355 GLN cc_start: 0.8157 (tp40) cc_final: 0.7742 (tp40)
REVERT: D  373 TYR cc_start: 0.8312 (m-10) cc_final: 0.8042 (m-80)
REVERT: D  377 ASN cc_start: 0.8637 (t0) cc_final: 0.8280 (t0)
REVERT: D  408 ASN cc_start: 0.8509 (t0) cc_final: 0.8206 (t0)
REVERT: D  414 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8048 (mt)
  outliers start: 34
  outliers final: 25
  residues processed: 262
  average time/residue: 0.2330
  time to fit residues: 77.1613
Evaluate side-chains
  271 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 239
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   25 CYS
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  155 ASP
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   80 HIS
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  394 ILE
Chi-restraints excluded: chain D residue  414 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0040
   chunk 0 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  56 HIS
G 105 GLN
G 139 HIS
D 212 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.144112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.118917 restraints weight = 12606.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.123241 restraints weight = 6735.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.126244 restraints weight = 4315.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7564  Z= 0.149
  Angle     :  0.670  11.690  10220  Z= 0.340
  Chirality :  0.045   0.313   1114
  Planarity :  0.004   0.041   1312
  Dihedral  :  4.474  25.203    978
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.43 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 30.15 %
    Favored  : 64.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.28), residues: 888
  helix:  1.12 (0.26), residues: 409
  sheet:  0.56 (0.58), residues: 81
  loop : -1.57 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP G   5 
 HIS   0.011   0.001   HIS A  10 
 PHE   0.021   0.002   PHE D 396 
 TYR   0.027   0.001   TYR B  79 
 ARG   0.005   0.001   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 (  318)
  hydrogen bonds       : angle       4.36748 (  957)
  covalent geometry    : bond        0.00348 ( 7564)
  covalent geometry    : angle       0.67017 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 243
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4187 (OUTLIER) cc_final: 0.3013 (mmt90)
REVERT: A   85 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6506 (t80)
REVERT: B   17 MET cc_start: 0.4597 (tpp) cc_final: 0.4299 (tpp)
REVERT: B   60 VAL cc_start: 0.8168 (p) cc_final: 0.7943 (p)
REVERT: C   54 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7080 (mt-10)
REVERT: C  113 TRP cc_start: 0.8394 (p-90) cc_final: 0.7752 (p-90)
REVERT: C  122 MET cc_start: 0.6790 (tpt) cc_final: 0.6334 (mmm)
REVERT: C  126 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6102 (mp0)
REVERT: C  140 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8445 (mt0)
REVERT: C  149 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8206 (mtm180)
REVERT: G    7 VAL cc_start: 0.8533 (t) cc_final: 0.8216 (m)
REVERT: G  135 TYR cc_start: 0.7912 (t80) cc_final: 0.7593 (t80)
REVERT: D   68 GLN cc_start: 0.7893 (pt0) cc_final: 0.7584 (tt0)
REVERT: D  102 ASN cc_start: 0.8522 (m-40) cc_final: 0.8247 (m-40)
REVERT: D  161 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8175 (mm)
REVERT: D  164 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7661 (mm-30)
REVERT: D  171 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6464 (mt-10)
REVERT: D  190 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7589 (tm-30)
REVERT: D  194 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: D  200 ASP cc_start: 0.8576 (t0) cc_final: 0.8301 (t0)
REVERT: D  203 GLU cc_start: 0.8073 (tt0) cc_final: 0.7654 (tt0)
REVERT: D  208 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8019 (ttpt)
REVERT: D  234 LEU cc_start: 0.8507 (mt) cc_final: 0.8208 (mt)
REVERT: D  258 ASN cc_start: 0.8450 (t0) cc_final: 0.8196 (t0)
REVERT: D  265 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7767 (mtmm)
REVERT: D  274 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6617 (mmtt)
REVERT: D  279 MET cc_start: 0.8358 (tpp) cc_final: 0.7935 (tpp)
REVERT: D  283 LYS cc_start: 0.8177 (tptt) cc_final: 0.7803 (tptt)
REVERT: D  285 LEU cc_start: 0.8294 (tt) cc_final: 0.7971 (tp)
REVERT: D  302 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7376 (mtpp)
REVERT: D  303 ASP cc_start: 0.7770 (t0) cc_final: 0.7550 (t0)
REVERT: D  320 LYS cc_start: 0.8270 (tppt) cc_final: 0.7450 (tppt)
REVERT: D  326 GLU cc_start: 0.6942 (tt0) cc_final: 0.6598 (tp30)
REVERT: D  335 GLU cc_start: 0.7654 (tp30) cc_final: 0.7292 (tp30)
REVERT: D  344 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7407 (mm-40)
REVERT: D  355 GLN cc_start: 0.8197 (tp40) cc_final: 0.7766 (tp40)
REVERT: D  370 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7851 (tpp-160)
REVERT: D  373 TYR cc_start: 0.8329 (m-10) cc_final: 0.8126 (m-80)
REVERT: D  377 ASN cc_start: 0.8632 (t0) cc_final: 0.8231 (t0)
REVERT: D  408 ASN cc_start: 0.8516 (t0) cc_final: 0.8114 (t0)
REVERT: D  414 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8066 (mt)
  outliers start: 42
  outliers final: 28
  residues processed: 265
  average time/residue: 0.2343
  time to fit residues: 78.2012
Evaluate side-chains
  273 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 239
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   25 CYS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain G residue    2 GLU
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   80 HIS
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain G residue  130 SER
Chi-restraints excluded: chain D residue   74 LYS
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  394 ILE
Chi-restraints excluded: chain D residue  414 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 58 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  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.143804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.119112 restraints weight = 12583.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.123380 restraints weight = 6713.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.126385 restraints weight = 4299.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7564  Z= 0.150
  Angle     :  0.683  10.885  10220  Z= 0.342
  Chirality :  0.044   0.271   1114
  Planarity :  0.004   0.039   1312
  Dihedral  :  4.484  25.860    978
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.21 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 30.89 %
    Favored  : 64.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.28), residues: 888
  helix:  1.06 (0.26), residues: 415
  sheet:  0.56 (0.59), residues: 81
  loop : -1.59 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G   5 
 HIS   0.012   0.001   HIS A  10 
 PHE   0.026   0.002   PHE D 396 
 TYR   0.031   0.002   TYR G  94 
 ARG   0.005   0.001   ARG D 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  318)
  hydrogen bonds       : angle       4.35034 (  957)
  covalent geometry    : bond        0.00350 ( 7564)
  covalent geometry    : angle       0.68285 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 247
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 PHE cc_start: 0.7285 (m-80) cc_final: 0.6948 (m-80)
REVERT: A   29 ARG cc_start: 0.4333 (OUTLIER) cc_final: 0.3173 (mmt90)
REVERT: B   17 MET cc_start: 0.4642 (tpp) cc_final: 0.4347 (tpp)
REVERT: B   60 VAL cc_start: 0.8157 (p) cc_final: 0.7940 (p)
REVERT: C   54 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6827 (mt-10)
REVERT: C  113 TRP cc_start: 0.8346 (p-90) cc_final: 0.7717 (p-90)
REVERT: C  122 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6349 (mmm)
REVERT: C  126 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6118 (mp0)
REVERT: C  149 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8207 (mtm180)
REVERT: G    7 VAL cc_start: 0.8459 (t) cc_final: 0.8167 (m)
REVERT: G  135 TYR cc_start: 0.7884 (t80) cc_final: 0.7519 (t80)
REVERT: G  141 LYS cc_start: 0.7548 (ttpt) cc_final: 0.7339 (mtpt)
REVERT: D   68 GLN cc_start: 0.7849 (pt0) cc_final: 0.7621 (tt0)
REVERT: D  102 ASN cc_start: 0.8553 (m-40) cc_final: 0.8268 (m-40)
REVERT: D  161 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8161 (mm)
REVERT: D  164 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7653 (mm-30)
REVERT: D  171 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6554 (mt-10)
REVERT: D  190 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7584 (tm-30)
REVERT: D  194 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7331 (mm-30)
REVERT: D  200 ASP cc_start: 0.8555 (t0) cc_final: 0.8292 (t0)
REVERT: D  208 LYS cc_start: 0.8442 (ttpt) cc_final: 0.7767 (ttpt)
REVERT: D  231 ASN cc_start: 0.8057 (m-40) cc_final: 0.7827 (m110)
REVERT: D  234 LEU cc_start: 0.8540 (mt) cc_final: 0.8239 (mt)
REVERT: D  251 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7036 (mt-10)
REVERT: D  258 ASN cc_start: 0.8433 (t0) cc_final: 0.8226 (t0)
REVERT: D  260 PHE cc_start: 0.7835 (m-10) cc_final: 0.7453 (m-80)
REVERT: D  265 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7735 (mtmm)
REVERT: D  274 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6540 (mmtt)
REVERT: D  279 MET cc_start: 0.8325 (tpp) cc_final: 0.7898 (tpp)
REVERT: D  283 LYS cc_start: 0.8172 (tptt) cc_final: 0.7825 (tptt)
REVERT: D  285 LEU cc_start: 0.8285 (tt) cc_final: 0.7960 (tp)
REVERT: D  302 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7342 (mtpp)
REVERT: D  326 GLU cc_start: 0.6917 (tt0) cc_final: 0.6567 (tp30)
REVERT: D  335 GLU cc_start: 0.7667 (tp30) cc_final: 0.7273 (tp30)
REVERT: D  344 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7390 (mm-40)
REVERT: D  355 GLN cc_start: 0.8174 (tp40) cc_final: 0.7759 (tp40)
REVERT: D  370 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7804 (tpp-160)
REVERT: D  373 TYR cc_start: 0.8287 (m-10) cc_final: 0.8056 (m-80)
REVERT: D  377 ASN cc_start: 0.8632 (t0) cc_final: 0.8242 (t0)
REVERT: D  408 ASN cc_start: 0.8509 (t0) cc_final: 0.8183 (t0)
REVERT: D  414 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8084 (mt)
  outliers start: 37
  outliers final: 28
  residues processed: 267
  average time/residue: 0.2689
  time to fit residues: 89.6143
Evaluate side-chains
  279 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 245
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   25 CYS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain G residue    2 GLU
Chi-restraints excluded: chain G residue    5 TRP
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   80 HIS
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  394 ILE
Chi-restraints excluded: chain D residue  414 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 105 GLN
D 212 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.140724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115988 restraints weight = 12579.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.120256 restraints weight = 6720.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.123222 restraints weight = 4302.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.5012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7564  Z= 0.204
  Angle     :  0.731  10.065  10220  Z= 0.370
  Chirality :  0.046   0.207   1114
  Planarity :  0.005   0.041   1312
  Dihedral  :  4.636  24.916    978
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.00 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 30.65 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.28), residues: 888
  helix:  1.01 (0.26), residues: 407
  sheet:  0.50 (0.59), residues: 81
  loop : -1.62 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP G   5 
 HIS   0.010   0.002   HIS A  10 
 PHE   0.022   0.002   PHE A  15 
 TYR   0.036   0.002   TYR B  79 
 ARG   0.010   0.001   ARG D 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04805 (  318)
  hydrogen bonds       : angle       4.54788 (  957)
  covalent geometry    : bond        0.00475 ( 7564)
  covalent geometry    : angle       0.73058 (10220)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 246
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 PHE cc_start: 0.7331 (m-80) cc_final: 0.6966 (m-80)
REVERT: A   29 ARG cc_start: 0.4665 (OUTLIER) cc_final: 0.3413 (mmt90)
REVERT: B   17 MET cc_start: 0.4720 (tpp) cc_final: 0.4430 (tpp)
REVERT: B   60 VAL cc_start: 0.8340 (p) cc_final: 0.8127 (p)
REVERT: C  113 TRP cc_start: 0.8363 (p-90) cc_final: 0.7777 (p-90)
REVERT: C  149 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8279 (mtm180)
REVERT: C  154 GLU cc_start: 0.7147 (tp30) cc_final: 0.6752 (tp30)
REVERT: G    7 VAL cc_start: 0.8557 (t) cc_final: 0.8291 (m)
REVERT: G   70 TRP cc_start: 0.7015 (p90) cc_final: 0.6602 (p90)
REVERT: G  135 TYR cc_start: 0.7947 (t80) cc_final: 0.7562 (t80)
REVERT: G  141 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7434 (mtpt)
REVERT: D  102 ASN cc_start: 0.8631 (m-40) cc_final: 0.8306 (m-40)
REVERT: D  133 ARG cc_start: 0.8367 (ptp90) cc_final: 0.8041 (ptt90)
REVERT: D  161 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8181 (mm)
REVERT: D  171 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6622 (mt-10)
REVERT: D  190 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: D  194 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7292 (mm-30)
REVERT: D  200 ASP cc_start: 0.8569 (t0) cc_final: 0.8290 (t0)
REVERT: D  208 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8047 (ttpt)
REVERT: D  231 ASN cc_start: 0.8088 (m-40) cc_final: 0.7865 (m110)
REVERT: D  234 LEU cc_start: 0.8551 (mt) cc_final: 0.8230 (mt)
REVERT: D  258 ASN cc_start: 0.8463 (t0) cc_final: 0.8230 (t0)
REVERT: D  260 PHE cc_start: 0.7852 (m-10) cc_final: 0.7486 (m-80)
REVERT: D  265 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7778 (mtmm)
REVERT: D  274 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6657 (mmtt)
REVERT: D  279 MET cc_start: 0.8311 (tpp) cc_final: 0.7844 (tpp)
REVERT: D  283 LYS cc_start: 0.8172 (tptt) cc_final: 0.7853 (tptt)
REVERT: D  285 LEU cc_start: 0.8311 (tt) cc_final: 0.7992 (tp)
REVERT: D  302 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7540 (mtpp)
REVERT: D  303 ASP cc_start: 0.7831 (t0) cc_final: 0.7544 (t0)
REVERT: D  326 GLU cc_start: 0.6953 (tt0) cc_final: 0.6595 (tp30)
REVERT: D  335 GLU cc_start: 0.7722 (tp30) cc_final: 0.7286 (tp30)
REVERT: D  344 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7471 (mm-40)
REVERT: D  370 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7935 (tpp-160)
REVERT: D  373 TYR cc_start: 0.8352 (m-10) cc_final: 0.8078 (m-80)
REVERT: D  374 PHE cc_start: 0.8665 (m-80) cc_final: 0.8281 (m-80)
REVERT: D  377 ASN cc_start: 0.8614 (t0) cc_final: 0.8071 (t0)
REVERT: D  408 ASN cc_start: 0.8449 (t0) cc_final: 0.8080 (t0)
REVERT: D  437 TYR cc_start: 0.6750 (t80) cc_final: 0.6489 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 264
  average time/residue: 0.2476
  time to fit residues: 82.3982
Evaluate side-chains
  270 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 242
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   25 CYS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain G residue    5 TRP
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  394 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 HIS
D 324 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.142243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.117433 restraints weight = 12432.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.121698 restraints weight = 6641.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.124661 restraints weight = 4261.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7564  Z= 0.153
  Angle     :  0.708   9.841  10220  Z= 0.356
  Chirality :  0.044   0.192   1114
  Planarity :  0.005   0.042   1312
  Dihedral  :  4.587  26.018    978
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.21 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 31.51 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.28), residues: 888
  helix:  1.01 (0.26), residues: 413
  sheet:  0.56 (0.61), residues: 76
  loop : -1.66 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP G   5 
 HIS   0.010   0.001   HIS A  10 
 PHE   0.019   0.002   PHE A  15 
 TYR   0.026   0.002   TYR B  79 
 ARG   0.010   0.001   ARG D 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04099 (  318)
  hydrogen bonds       : angle       4.44477 (  957)
  covalent geometry    : bond        0.00359 ( 7564)
  covalent geometry    : angle       0.70756 (10220)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2835.39 seconds
wall clock time: 50 minutes 34.32 seconds (3034.32 seconds total)