Starting phenix.real_space_refine
on Fri Oct 10 15:45:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8szk_40919/10_2025/8szk_40919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8szk_40919/10_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_40919/10_2025/8szk_40919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8szk_40919/10_2025/8szk_40919.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8szk_40919/10_2025/8szk_40919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8szk_40919/10_2025/8szk_40919.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 2}
          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: 2.08, per 1000 atoms: 0.28
  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: 0.70
  Conformation dependent library (CDL) restraints added in 407.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.26
  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: 1.16

  Time building geometry restraints manager: 0.91 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:             0.550
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.840
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.960
-------------------------------------------------------------------------------
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 : 17.94
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.001   ARG A  43 
 TYR   0.025   0.002   TYR D 437 
 PHE   0.039   0.002   PHE A  79 
 TRP   0.024   0.002   TRP G   5 
 HIS   0.013   0.002   HIS G  73 

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

*********************** 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  : 0.286 
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: 0.1166
  time to fit residues: 42.1942
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  : 0.289 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0060
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.9600

-------------------------------------------------------------------------------
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
C  63 ASN
G  28 HIS
G  43 HIS
G  73 HIS
G 108 HIS
D  58 GLN
D  73 GLN
D  77 GLN
D 212 HIS
D 228 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.147778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.121852 restraints weight = 12489.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.126147 restraints weight = 6815.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.129094 restraints weight = 4438.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.131166 restraints weight = 3251.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.132485 restraints weight = 2599.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7564  Z= 0.193
  Angle     :  0.745   7.955  10220  Z= 0.391
  Chirality :  0.047   0.251   1114
  Planarity :  0.005   0.044   1312
  Dihedral  :  4.931  30.153    981
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.21 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 27.42 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.28), residues: 888
  helix:  0.69 (0.26), residues: 416
  sheet:  0.56 (0.53), residues: 88
  loop : -1.56 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  37 
 TYR   0.021   0.002   TYR B  79 
 PHE   0.022   0.002   PHE G 112 
 TRP   0.031   0.002   TRP G   5 
 HIS   0.012   0.002   HIS G  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7564)
  covalent geometry    : angle       0.74533 (10220)
  hydrogen bonds       : bond        0.05950 (  318)
  hydrogen bonds       : angle       5.21991 (  957)

*********************** 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
  312 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 266
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 HIS cc_start: 0.6984 (m-70) cc_final: 0.5979 (m-70)
REVERT: B   30 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7617 (mt)
REVERT: C   54 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7060 (mt-10)
REVERT: C   91 GLU cc_start: 0.6704 (mp0) cc_final: 0.5845 (mp0)
REVERT: C  126 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5875 (mp0)
REVERT: C  149 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7767 (mtm180)
REVERT: G    5 TRP cc_start: 0.6913 (m-10) cc_final: 0.6516 (m-10)
REVERT: G  107 ILE cc_start: 0.7742 (tt) cc_final: 0.7526 (tt)
REVERT: G  167 ARG cc_start: 0.7349 (ttp80) cc_final: 0.7147 (ttp80)
REVERT: D   68 GLN cc_start: 0.7722 (pt0) cc_final: 0.7347 (tt0)
REVERT: D   69 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6136 (tm-30)
REVERT: D   73 GLN cc_start: 0.7953 (mt0) cc_final: 0.7476 (mt0)
REVERT: D  107 TYR cc_start: 0.7903 (t80) cc_final: 0.7677 (t80)
REVERT: D  115 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8078 (tp)
REVERT: D  126 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7548 (tpt)
REVERT: D  127 ILE cc_start: 0.8156 (mm) cc_final: 0.7924 (mt)
REVERT: D  161 LEU cc_start: 0.8438 (mm) cc_final: 0.8124 (mm)
REVERT: D  171 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6557 (mt-10)
REVERT: D  194 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7331 (mm-30)
REVERT: D  208 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7721 (ttpt)
REVERT: D  209 THR cc_start: 0.8328 (m) cc_final: 0.8091 (t)
REVERT: D  248 GLU cc_start: 0.7369 (mp0) cc_final: 0.6427 (mp0)
REVERT: D  251 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7102 (mt-10)
REVERT: D  258 ASN cc_start: 0.8669 (t0) cc_final: 0.8443 (t0)
REVERT: D  265 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7798 (mtmm)
REVERT: D  274 LYS cc_start: 0.6938 (mmtt) cc_final: 0.6594 (mmtt)
REVERT: D  283 LYS cc_start: 0.8299 (tptt) cc_final: 0.7871 (tptt)
REVERT: D  285 LEU cc_start: 0.8243 (tt) cc_final: 0.7941 (tp)
REVERT: D  301 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6798 (tm-30)
REVERT: D  335 GLU cc_start: 0.7570 (tp30) cc_final: 0.7256 (tp30)
REVERT: D  344 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7327 (mm-40)
REVERT: D  355 GLN cc_start: 0.8221 (tp40) cc_final: 0.7792 (tp40)
REVERT: D  377 ASN cc_start: 0.8695 (t0) cc_final: 0.8334 (t0)
REVERT: D  385 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6423 (mm-30)
REVERT: D  389 ASP cc_start: 0.7559 (p0) cc_final: 0.7344 (p0)
REVERT: D  398 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8627 (t)
REVERT: D  408 ASN cc_start: 0.8289 (t0) cc_final: 0.7772 (t0)
REVERT: D  429 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7719 (tt)
  outliers start: 46
  outliers final: 21
  residues processed: 292
  average time/residue: 0.1142
  time to fit residues: 42.1859
Evaluate side-chains
  281 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 253
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   22 SER
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 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  114 CYS
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain D residue   83 ASP
Chi-restraints excluded: chain D residue  115 ILE
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  328 MET
Chi-restraints excluded: chain D residue  398 SER
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 57 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0000
   chunk 4 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0070
   chunk 81 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.9806

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
G 105 GLN
G 139 HIS
G 146 GLN
D 212 HIS
D 387 ASN
D 406 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.145356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119810 restraints weight = 12458.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.124162 restraints weight = 6782.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127081 restraints weight = 4362.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.129197 restraints weight = 3172.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.130599 restraints weight = 2506.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7564  Z= 0.174
  Angle     :  0.674   7.164  10220  Z= 0.355
  Chirality :  0.046   0.264   1114
  Planarity :  0.005   0.089   1312
  Dihedral  :  4.671  29.923    978
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.21 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 27.92 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.28), residues: 888
  helix:  0.84 (0.26), residues: 414
  sheet:  0.52 (0.60), residues: 67
  loop : -1.73 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A   9 
 TYR   0.024   0.002   TYR B  79 
 PHE   0.029   0.002   PHE A  15 
 TRP   0.021   0.001   TRP G   5 
 HIS   0.018   0.002   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 7564)
  covalent geometry    : angle       0.67388 (10220)
  hydrogen bonds       : bond        0.05328 (  318)
  hydrogen bonds       : angle       4.77830 (  957)

*********************** 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
  303 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 262
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.6895 (tmm-80) cc_final: 0.6398 (tmm-80)
REVERT: A   70 GLN cc_start: 0.7673 (mp10) cc_final: 0.7388 (mp10)
REVERT: B   30 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7589 (mt)
REVERT: C   24 GLU cc_start: 0.6458 (tp30) cc_final: 0.6232 (tp30)
REVERT: C  113 TRP cc_start: 0.8395 (p-90) cc_final: 0.7646 (p-90)
REVERT: C  126 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5798 (mp0)
REVERT: C  149 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8096 (mtm180)
REVERT: G    7 VAL cc_start: 0.8536 (t) cc_final: 0.8272 (m)
REVERT: G   70 TRP cc_start: 0.6972 (p90) cc_final: 0.6587 (p90)
REVERT: G   97 GLN cc_start: 0.8616 (mp10) cc_final: 0.8161 (mm-40)
REVERT: G  107 ILE cc_start: 0.7647 (tt) cc_final: 0.7412 (tt)
REVERT: D   68 GLN cc_start: 0.7702 (pt0) cc_final: 0.7389 (tt0)
REVERT: D   73 GLN cc_start: 0.7919 (mt0) cc_final: 0.7576 (mt0)
REVERT: D  107 TYR cc_start: 0.7984 (t80) cc_final: 0.7750 (t80)
REVERT: D  125 LYS cc_start: 0.8179 (mttm) cc_final: 0.7955 (mtmm)
REVERT: D  126 MET cc_start: 0.7806 (tpt) cc_final: 0.7605 (tpt)
REVERT: D  161 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8147 (mm)
REVERT: D  164 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7696 (mm-30)
REVERT: D  171 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6518 (mt-10)
REVERT: D  194 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7341 (mm-30)
REVERT: D  200 ASP cc_start: 0.8568 (t0) cc_final: 0.8320 (t0)
REVERT: D  208 LYS cc_start: 0.8300 (ttpt) cc_final: 0.7666 (ttpt)
REVERT: D  248 GLU cc_start: 0.7350 (mp0) cc_final: 0.6422 (mp0)
REVERT: D  251 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7078 (mt-10)
REVERT: D  258 ASN cc_start: 0.8564 (t0) cc_final: 0.8363 (t0)
REVERT: D  265 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7860 (mtmm)
REVERT: D  274 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6637 (mmtt)
REVERT: D  283 LYS cc_start: 0.8292 (tptt) cc_final: 0.7840 (tptt)
REVERT: D  285 LEU cc_start: 0.8316 (tt) cc_final: 0.8009 (tp)
REVERT: D  312 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7774 (mtt-85)
REVERT: D  335 GLU cc_start: 0.7622 (tp30) cc_final: 0.7207 (tp30)
REVERT: D  344 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7134 (mm-40)
REVERT: D  347 LYS cc_start: 0.7924 (mttp) cc_final: 0.7329 (mttp)
REVERT: D  355 GLN cc_start: 0.8250 (tp40) cc_final: 0.7790 (tp40)
REVERT: D  373 TYR cc_start: 0.8343 (m-10) cc_final: 0.8079 (m-80)
REVERT: D  377 ASN cc_start: 0.8732 (t0) cc_final: 0.8427 (t0)
REVERT: D  386 GLU cc_start: 0.7472 (tp30) cc_final: 0.7267 (tp30)
REVERT: D  408 ASN cc_start: 0.8507 (t0) cc_final: 0.8263 (t0)
REVERT: D  415 VAL cc_start: 0.8519 (t) cc_final: 0.8312 (p)
  outliers start: 41
  outliers final: 23
  residues processed: 281
  average time/residue: 0.1110
  time to fit residues: 39.1518
Evaluate side-chains
  281 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 255
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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   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   17 PHE
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  114 CYS
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  225 ILE
Chi-restraints excluded: chain D residue  271 PHE
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.143847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.118279 restraints weight = 12500.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.122580 restraints weight = 6732.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.125541 restraints weight = 4339.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.127555 restraints weight = 3151.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.128922 restraints weight = 2504.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7564  Z= 0.185
  Angle     :  0.673   7.566  10220  Z= 0.351
  Chirality :  0.045   0.175   1114
  Planarity :  0.005   0.041   1312
  Dihedral  :  4.693  26.327    978
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.43 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 27.92 %
    Favored  : 65.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.28), residues: 888
  helix:  0.94 (0.26), residues: 407
  sheet:  0.38 (0.58), residues: 81
  loop : -1.73 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 226 
 TYR   0.028   0.002   TYR B  79 
 PHE   0.025   0.002   PHE D 396 
 TRP   0.015   0.001   TRP G   5 
 HIS   0.012   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 7564)
  covalent geometry    : angle       0.67302 (10220)
  hydrogen bonds       : bond        0.04936 (  318)
  hydrogen bonds       : angle       4.68302 (  957)

*********************** 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
  306 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 255
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4120 (OUTLIER) cc_final: 0.2868 (mmt90)
REVERT: B   30 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7695 (mt)
REVERT: C   24 GLU cc_start: 0.6724 (tp30) cc_final: 0.6477 (tp30)
REVERT: C  113 TRP cc_start: 0.8403 (p-90) cc_final: 0.7726 (p-90)
REVERT: C  122 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6231 (tpp)
REVERT: C  126 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5974 (mp0)
REVERT: C  140 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8299 (mm-40)
REVERT: C  149 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8230 (mtm180)
REVERT: G    7 VAL cc_start: 0.8568 (t) cc_final: 0.8288 (m)
REVERT: G   70 TRP cc_start: 0.7257 (p90) cc_final: 0.6947 (p90)
REVERT: G   97 GLN cc_start: 0.8644 (mp10) cc_final: 0.8193 (mm-40)
REVERT: G  107 ILE cc_start: 0.7740 (tt) cc_final: 0.7492 (tt)
REVERT: G  127 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7375 (mtt180)
REVERT: D   68 GLN cc_start: 0.7766 (pt0) cc_final: 0.7419 (tt0)
REVERT: D   73 GLN cc_start: 0.7953 (mt0) cc_final: 0.7621 (mt0)
REVERT: D  107 TYR cc_start: 0.8013 (t80) cc_final: 0.7642 (t80)
REVERT: D  125 LYS cc_start: 0.8150 (mttm) cc_final: 0.7936 (mtmm)
REVERT: D  126 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7502 (tpt)
REVERT: D  161 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8171 (mm)
REVERT: D  164 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7691 (mm-30)
REVERT: D  171 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6546 (mt-10)
REVERT: D  194 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7320 (mm-30)
REVERT: D  200 ASP cc_start: 0.8566 (t0) cc_final: 0.8324 (t0)
REVERT: D  208 LYS cc_start: 0.8352 (ttpt) cc_final: 0.7516 (ttpt)
REVERT: D  248 GLU cc_start: 0.7362 (mp0) cc_final: 0.6554 (mp0)
REVERT: D  251 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6914 (mt-10)
REVERT: D  258 ASN cc_start: 0.8559 (t0) cc_final: 0.8280 (t0)
REVERT: D  265 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7806 (mtmm)
REVERT: D  274 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6608 (mmtt)
REVERT: D  283 LYS cc_start: 0.8209 (tptt) cc_final: 0.7797 (tptt)
REVERT: D  285 LEU cc_start: 0.8351 (tt) cc_final: 0.7969 (tp)
REVERT: D  326 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6551 (tp30)
REVERT: D  335 GLU cc_start: 0.7599 (tp30) cc_final: 0.7140 (tp30)
REVERT: D  344 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7368 (mm-40)
REVERT: D  373 TYR cc_start: 0.8352 (m-10) cc_final: 0.8095 (m-80)
REVERT: D  377 ASN cc_start: 0.8754 (t0) cc_final: 0.8485 (t0)
REVERT: D  396 PHE cc_start: 0.8300 (t80) cc_final: 0.8090 (t80)
REVERT: D  398 SER cc_start: 0.8870 (m) cc_final: 0.8556 (t)
REVERT: D  408 ASN cc_start: 0.8503 (t0) cc_final: 0.8270 (t0)
REVERT: D  415 VAL cc_start: 0.8580 (t) cc_final: 0.8341 (p)
  outliers start: 51
  outliers final: 27
  residues processed: 276
  average time/residue: 0.1176
  time to fit residues: 40.5001
Evaluate side-chains
  285 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 251
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   17 PHE
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  129 VAL
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  126 MET
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  225 ILE
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  306 LEU
Chi-restraints excluded: chain D residue  326 GLU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 70 optimal weight:    0.1980
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
C 140 GLN
G  56 HIS
G 105 GLN
** D 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.145150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.119761 restraints weight = 12424.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.124061 restraints weight = 6690.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127038 restraints weight = 4303.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.128987 restraints weight = 3119.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130410 restraints weight = 2481.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7564  Z= 0.136
  Angle     :  0.637   9.599  10220  Z= 0.329
  Chirality :  0.044   0.240   1114
  Planarity :  0.004   0.038   1312
  Dihedral  :  4.630  28.874    978
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.43 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 28.16 %
    Favored  : 65.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.28), residues: 888
  helix:  1.11 (0.26), residues: 406
  sheet:  0.41 (0.58), residues: 81
  loop : -1.64 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A   8 
 TYR   0.021   0.001   TYR B  79 
 PHE   0.016   0.002   PHE D 396 
 TRP   0.024   0.001   TRP D 375 
 HIS   0.007   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7564)
  covalent geometry    : angle       0.63721 (10220)
  hydrogen bonds       : bond        0.04227 (  318)
  hydrogen bonds       : angle       4.50160 (  957)

*********************** 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
  296 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 247
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4073 (OUTLIER) cc_final: 0.2837 (mmt90)
REVERT: B   30 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7655 (mt)
REVERT: B   60 VAL cc_start: 0.8293 (p) cc_final: 0.8083 (p)
REVERT: C   24 GLU cc_start: 0.6727 (tp30) cc_final: 0.6473 (tp30)
REVERT: C  113 TRP cc_start: 0.8377 (p-90) cc_final: 0.7721 (p-90)
REVERT: C  122 MET cc_start: 0.6648 (tpt) cc_final: 0.6032 (tpp)
REVERT: C  126 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5955 (mp0)
REVERT: C  149 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8248 (mtm180)
REVERT: G    7 VAL cc_start: 0.8584 (t) cc_final: 0.8278 (m)
REVERT: G   70 TRP cc_start: 0.7032 (p90) cc_final: 0.6682 (p90)
REVERT: G   97 GLN cc_start: 0.8614 (mp10) cc_final: 0.8117 (mm-40)
REVERT: G  107 ILE cc_start: 0.7783 (tt) cc_final: 0.7513 (tt)
REVERT: D   68 GLN cc_start: 0.7732 (pt0) cc_final: 0.7387 (tt0)
REVERT: D   73 GLN cc_start: 0.7953 (mt0) cc_final: 0.7622 (mt0)
REVERT: D   77 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (tm-30)
REVERT: D  125 LYS cc_start: 0.8165 (mttm) cc_final: 0.7921 (mtmm)
REVERT: D  126 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7518 (tpt)
REVERT: D  161 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8199 (mm)
REVERT: D  164 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7603 (mm-30)
REVERT: D  171 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6440 (mt-10)
REVERT: D  190 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: D  194 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7295 (mm-30)
REVERT: D  200 ASP cc_start: 0.8538 (t0) cc_final: 0.8315 (t0)
REVERT: D  208 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8052 (ttpt)
REVERT: D  234 LEU cc_start: 0.8390 (mt) cc_final: 0.8062 (mt)
REVERT: D  258 ASN cc_start: 0.8517 (t0) cc_final: 0.8299 (t0)
REVERT: D  265 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7778 (mtmm)
REVERT: D  274 LYS cc_start: 0.6924 (mmtt) cc_final: 0.6546 (mmtt)
REVERT: D  279 MET cc_start: 0.8364 (tpp) cc_final: 0.7905 (tpp)
REVERT: D  283 LYS cc_start: 0.8195 (tptt) cc_final: 0.7785 (tptt)
REVERT: D  285 LEU cc_start: 0.8314 (tt) cc_final: 0.7976 (tp)
REVERT: D  302 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7492 (mtpp)
REVERT: D  326 GLU cc_start: 0.6829 (tt0) cc_final: 0.6482 (tp30)
REVERT: D  335 GLU cc_start: 0.7561 (tp30) cc_final: 0.7219 (tp30)
REVERT: D  344 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7302 (mm-40)
REVERT: D  355 GLN cc_start: 0.8169 (tp40) cc_final: 0.7721 (tp40)
REVERT: D  373 TYR cc_start: 0.8300 (m-10) cc_final: 0.8042 (m-80)
REVERT: D  377 ASN cc_start: 0.8713 (t0) cc_final: 0.8381 (t0)
REVERT: D  396 PHE cc_start: 0.8301 (t80) cc_final: 0.8089 (t80)
REVERT: D  398 SER cc_start: 0.8849 (m) cc_final: 0.8574 (t)
REVERT: D  408 ASN cc_start: 0.8514 (t0) cc_final: 0.8277 (t0)
REVERT: D  415 VAL cc_start: 0.8586 (t) cc_final: 0.8315 (p)
  outliers start: 49
  outliers final: 27
  residues processed: 275
  average time/residue: 0.1120
  time to fit residues: 39.1514
Evaluate side-chains
  273 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 240
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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 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   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    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  116 SER
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  126 MET
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 87 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 105 GLN
** D 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.142687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.117181 restraints weight = 12558.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121443 restraints weight = 6801.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.124335 restraints weight = 4402.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.126351 restraints weight = 3214.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.127604 restraints weight = 2567.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.4439

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= 0.186
  Angle     :  0.681  10.314  10220  Z= 0.350
  Chirality :  0.046   0.255   1114
  Planarity :  0.005   0.038   1312
  Dihedral  :  4.611  26.969    978
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.66 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 27.79 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.28), residues: 888
  helix:  1.12 (0.26), residues: 406
  sheet:  0.22 (0.59), residues: 82
  loop : -1.60 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A   8 
 TYR   0.034   0.002   TYR B  79 
 PHE   0.018   0.002   PHE B  77 
 TRP   0.013   0.002   TRP G   5 
 HIS   0.006   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 7564)
  covalent geometry    : angle       0.68085 (10220)
  hydrogen bonds       : bond        0.04682 (  318)
  hydrogen bonds       : angle       4.58793 (  957)

*********************** 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
  296 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 248
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.3415 (mmt90)
REVERT: B   30 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7688 (mt)
REVERT: B   60 VAL cc_start: 0.8181 (p) cc_final: 0.7963 (p)
REVERT: B   74 CYS cc_start: 0.7767 (t) cc_final: 0.7423 (t)
REVERT: C   26 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6349 (mm-30)
REVERT: C  113 TRP cc_start: 0.8386 (p-90) cc_final: 0.7775 (p-90)
REVERT: C  122 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6343 (mmm)
REVERT: C  126 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.6078 (mp0)
REVERT: C  140 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8417 (mt0)
REVERT: C  149 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8301 (mtm180)
REVERT: G    7 VAL cc_start: 0.8438 (t) cc_final: 0.8189 (m)
REVERT: G   69 TYR cc_start: 0.7678 (m-10) cc_final: 0.7244 (m-80)
REVERT: G   70 TRP cc_start: 0.7240 (p90) cc_final: 0.6863 (p90)
REVERT: G   97 GLN cc_start: 0.8621 (mp10) cc_final: 0.8167 (mm-40)
REVERT: G  107 ILE cc_start: 0.7820 (tt) cc_final: 0.7559 (tt)
REVERT: G  135 TYR cc_start: 0.7924 (t80) cc_final: 0.7517 (t80)
REVERT: D   68 GLN cc_start: 0.7750 (pt0) cc_final: 0.7455 (tt0)
REVERT: D   69 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6699 (tm-30)
REVERT: D   77 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8275 (tm-30)
REVERT: D  107 TYR cc_start: 0.8151 (t80) cc_final: 0.7744 (t80)
REVERT: D  125 LYS cc_start: 0.8183 (mttm) cc_final: 0.7956 (mtmm)
REVERT: D  161 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8192 (mm)
REVERT: D  164 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7698 (mm-30)
REVERT: D  171 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6507 (mt-10)
REVERT: D  190 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7528 (tm-30)
REVERT: D  194 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7290 (mm-30)
REVERT: D  200 ASP cc_start: 0.8553 (t0) cc_final: 0.8330 (t0)
REVERT: D  203 GLU cc_start: 0.8133 (tt0) cc_final: 0.7630 (tt0)
REVERT: D  208 LYS cc_start: 0.8435 (ttpt) cc_final: 0.7708 (ttpt)
REVERT: D  234 LEU cc_start: 0.8473 (mt) cc_final: 0.8150 (mt)
REVERT: D  251 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7044 (mt-10)
REVERT: D  258 ASN cc_start: 0.8454 (t0) cc_final: 0.8206 (t0)
REVERT: D  265 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7790 (mtmm)
REVERT: D  274 LYS cc_start: 0.6922 (mmtt) cc_final: 0.6553 (mmtt)
REVERT: D  279 MET cc_start: 0.8336 (tpp) cc_final: 0.7874 (tpp)
REVERT: D  283 LYS cc_start: 0.8194 (tptt) cc_final: 0.7797 (tptt)
REVERT: D  285 LEU cc_start: 0.8328 (tt) cc_final: 0.7981 (tp)
REVERT: D  302 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7435 (mtpp)
REVERT: D  326 GLU cc_start: 0.6870 (tt0) cc_final: 0.6534 (tp30)
REVERT: D  334 GLU cc_start: 0.8124 (tt0) cc_final: 0.7807 (tt0)
REVERT: D  335 GLU cc_start: 0.7604 (tp30) cc_final: 0.7234 (tp30)
REVERT: D  344 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7387 (mm-40)
REVERT: D  373 TYR cc_start: 0.8320 (m-10) cc_final: 0.8089 (m-80)
REVERT: D  377 ASN cc_start: 0.8703 (t0) cc_final: 0.8400 (t0)
REVERT: D  396 PHE cc_start: 0.8175 (t80) cc_final: 0.7937 (t80)
REVERT: D  398 SER cc_start: 0.8724 (m) cc_final: 0.8475 (t)
REVERT: D  408 ASN cc_start: 0.8514 (t0) cc_final: 0.8199 (t0)
  outliers start: 48
  outliers final: 32
  residues processed: 275
  average time/residue: 0.1148
  time to fit residues: 40.0347
Evaluate side-chains
  283 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 245
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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   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   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    2 GLU
Chi-restraints excluded: chain G residue    3 ASN
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   77 GLN
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  109 SER
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0040
   chunk 87 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:   20.0000
   overall best weight:    1.7598

-------------------------------------------------------------------------------
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 268 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 = 0.3838 r_free = 0.3838 target = 0.139389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114377 restraints weight = 12339.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118617 restraints weight = 6640.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121513 restraints weight = 4268.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.123489 restraints weight = 3098.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.124723 restraints weight = 2462.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   7564  Z= 0.253
  Angle     :  0.744  10.647  10220  Z= 0.387
  Chirality :  0.048   0.267   1114
  Planarity :  0.005   0.053   1312
  Dihedral  :  4.883  29.812    978
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.22 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 28.29 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.28), residues: 888
  helix:  0.79 (0.25), residues: 407
  sheet:  0.07 (0.62), residues: 77
  loop : -1.51 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 182 
 TYR   0.044   0.002   TYR B  79 
 PHE   0.022   0.003   PHE C  44 
 TRP   0.023   0.002   TRP G   5 
 HIS   0.010   0.002   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 7564)
  covalent geometry    : angle       0.74419 (10220)
  hydrogen bonds       : bond        0.05457 (  318)
  hydrogen bonds       : angle       4.81941 (  957)

*********************** 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
  302 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 255
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.3477 (mmt90)
REVERT: B   17 MET cc_start: 0.4855 (tpp) cc_final: 0.4619 (tpp)
REVERT: B   60 VAL cc_start: 0.8282 (p) cc_final: 0.8077 (p)
REVERT: B   74 CYS cc_start: 0.7752 (t) cc_final: 0.7496 (t)
REVERT: C   54 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6893 (mt-10)
REVERT: C  113 TRP cc_start: 0.8375 (p-90) cc_final: 0.7799 (p-90)
REVERT: C  149 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8321 (mtm180)
REVERT: G   34 LYS cc_start: 0.8575 (mttm) cc_final: 0.8295 (mttm)
REVERT: G   41 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.6735 (mtm-85)
REVERT: G   69 TYR cc_start: 0.7801 (m-10) cc_final: 0.7275 (m-80)
REVERT: G   70 TRP cc_start: 0.7653 (p90) cc_final: 0.7404 (p90)
REVERT: G   97 GLN cc_start: 0.8632 (mp10) cc_final: 0.8332 (mm-40)
REVERT: G  107 ILE cc_start: 0.7861 (tt) cc_final: 0.7564 (tt)
REVERT: D   68 GLN cc_start: 0.7766 (pt0) cc_final: 0.7481 (tt0)
REVERT: D  107 TYR cc_start: 0.8231 (t80) cc_final: 0.7767 (t80)
REVERT: D  125 LYS cc_start: 0.8185 (mttm) cc_final: 0.7857 (mtmm)
REVERT: D  161 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (mm)
REVERT: D  164 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7730 (mm-30)
REVERT: D  171 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6684 (mt-10)
REVERT: D  190 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7510 (tm-30)
REVERT: D  194 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7302 (mm-30)
REVERT: D  200 ASP cc_start: 0.8576 (t0) cc_final: 0.8294 (t0)
REVERT: D  208 LYS cc_start: 0.8421 (ttpt) cc_final: 0.7817 (ttpt)
REVERT: D  234 LEU cc_start: 0.8504 (mt) cc_final: 0.8193 (mt)
REVERT: D  251 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7125 (mt-10)
REVERT: D  258 ASN cc_start: 0.8469 (t0) cc_final: 0.8190 (t0)
REVERT: D  260 PHE cc_start: 0.7814 (m-10) cc_final: 0.7366 (m-80)
REVERT: D  265 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7849 (mtmm)
REVERT: D  274 LYS cc_start: 0.6980 (mmtt) cc_final: 0.6594 (mmtt)
REVERT: D  279 MET cc_start: 0.8314 (tpp) cc_final: 0.7874 (tpp)
REVERT: D  283 LYS cc_start: 0.8208 (tptt) cc_final: 0.7816 (tptt)
REVERT: D  285 LEU cc_start: 0.8322 (tt) cc_final: 0.7981 (tp)
REVERT: D  302 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7487 (mtpp)
REVERT: D  326 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6594 (tp30)
REVERT: D  335 GLU cc_start: 0.7627 (tp30) cc_final: 0.7226 (tp30)
REVERT: D  344 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7483 (mm-40)
REVERT: D  373 TYR cc_start: 0.8359 (m-10) cc_final: 0.8062 (m-80)
REVERT: D  377 ASN cc_start: 0.8761 (t0) cc_final: 0.8409 (t0)
REVERT: D  398 SER cc_start: 0.8714 (m) cc_final: 0.8372 (t)
REVERT: D  408 ASN cc_start: 0.8521 (t0) cc_final: 0.8218 (t0)
  outliers start: 47
  outliers final: 29
  residues processed: 275
  average time/residue: 0.1251
  time to fit residues: 42.8474
Evaluate side-chains
  285 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 252
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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   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 G residue    3 ASN
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 G residue  154 ILE
Chi-restraints excluded: chain G residue  169 LEU
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  304 THR
Chi-restraints excluded: chain D residue  326 GLU
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  395 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0470
   chunk 76 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0870
   overall best weight:    0.4458

-------------------------------------------------------------------------------
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**
D  77 GLN
D 212 HIS
D 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.143475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.118437 restraints weight = 12382.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.122743 restraints weight = 6601.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.125704 restraints weight = 4228.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.127750 restraints weight = 3052.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.129019 restraints weight = 2409.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.4988

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= 0.131
  Angle     :  0.678   9.743  10220  Z= 0.345
  Chirality :  0.043   0.169   1114
  Planarity :  0.005   0.068   1312
  Dihedral  :  4.699  28.213    978
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.43 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 30.15 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.29), residues: 888
  helix:  1.11 (0.26), residues: 399
  sheet:  0.30 (0.63), residues: 76
  loop : -1.49 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 441 
 TYR   0.016   0.001   TYR B  79 
 PHE   0.029   0.002   PHE D 396 
 TRP   0.014   0.001   TRP D 375 
 HIS   0.011   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7564)
  covalent geometry    : angle       0.67837 (10220)
  hydrogen bonds       : bond        0.03967 (  318)
  hydrogen bonds       : angle       4.50261 (  957)

*********************** 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
  279 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 242
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4615 (OUTLIER) cc_final: 0.3168 (mmt90)
REVERT: B   17 MET cc_start: 0.4931 (tpp) cc_final: 0.4637 (tpp)
REVERT: B   60 VAL cc_start: 0.8095 (p) cc_final: 0.7884 (p)
REVERT: B   74 CYS cc_start: 0.7745 (t) cc_final: 0.7263 (t)
REVERT: C   54 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6894 (mt-10)
REVERT: C  113 TRP cc_start: 0.8352 (p-90) cc_final: 0.7778 (p-90)
REVERT: C  147 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7741 (ttp80)
REVERT: C  149 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8304 (mtm180)
REVERT: G   70 TRP cc_start: 0.7310 (p90) cc_final: 0.7044 (p90)
REVERT: G   97 GLN cc_start: 0.8585 (mp10) cc_final: 0.8193 (mm-40)
REVERT: G  107 ILE cc_start: 0.7783 (tt) cc_final: 0.7490 (tt)
REVERT: D   68 GLN cc_start: 0.7688 (pt0) cc_final: 0.7475 (tt0)
REVERT: D   69 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6558 (tm-30)
REVERT: D  102 ASN cc_start: 0.8487 (m-40) cc_final: 0.8206 (m-40)
REVERT: D  125 LYS cc_start: 0.8110 (mttm) cc_final: 0.7898 (mtmm)
REVERT: D  161 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8191 (mm)
REVERT: D  164 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7646 (mm-30)
REVERT: D  171 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6483 (mt-10)
REVERT: D  190 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7457 (tm-30)
REVERT: D  194 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7248 (mm-30)
REVERT: D  200 ASP cc_start: 0.8499 (t0) cc_final: 0.8224 (t0)
REVERT: D  208 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7825 (ttpt)
REVERT: D  234 LEU cc_start: 0.8468 (mt) cc_final: 0.8142 (mt)
REVERT: D  258 ASN cc_start: 0.8399 (t0) cc_final: 0.8101 (t0)
REVERT: D  260 PHE cc_start: 0.7818 (m-10) cc_final: 0.7233 (m-80)
REVERT: D  265 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7731 (mtmm)
REVERT: D  274 LYS cc_start: 0.6998 (mmtt) cc_final: 0.6565 (mmtt)
REVERT: D  279 MET cc_start: 0.8272 (tpp) cc_final: 0.7851 (tpp)
REVERT: D  283 LYS cc_start: 0.8167 (tptt) cc_final: 0.7782 (tptt)
REVERT: D  285 LEU cc_start: 0.8224 (tt) cc_final: 0.7904 (tp)
REVERT: D  302 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7558 (ttmm)
REVERT: D  326 GLU cc_start: 0.6735 (tt0) cc_final: 0.6395 (tp30)
REVERT: D  335 GLU cc_start: 0.7598 (tp30) cc_final: 0.7187 (tp30)
REVERT: D  344 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7406 (mm-40)
REVERT: D  373 TYR cc_start: 0.8261 (m-10) cc_final: 0.7956 (m-80)
REVERT: D  377 ASN cc_start: 0.8757 (t0) cc_final: 0.8181 (t0)
REVERT: D  398 SER cc_start: 0.8718 (m) cc_final: 0.8298 (t)
REVERT: D  401 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8049 (tttm)
REVERT: D  408 ASN cc_start: 0.8506 (t0) cc_final: 0.8227 (t0)
REVERT: D  415 VAL cc_start: 0.8507 (m) cc_final: 0.8291 (p)
  outliers start: 37
  outliers final: 25
  residues processed: 258
  average time/residue: 0.1142
  time to fit residues: 37.1492
Evaluate side-chains
  265 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 236
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 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  163 TYR
Chi-restraints excluded: chain D residue  253 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
Chi-restraints excluded: chain D residue  401 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 73 optimal weight:    0.3980
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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**
D  77 GLN
D 212 HIS
D 231 ASN
D 387 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.142959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.118049 restraints weight = 12200.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.122295 restraints weight = 6527.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125265 restraints weight = 4190.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.127260 restraints weight = 3028.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.128652 restraints weight = 2396.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.5093

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= 0.145
  Angle     :  0.690   9.503  10220  Z= 0.349
  Chirality :  0.044   0.167   1114
  Planarity :  0.005   0.066   1312
  Dihedral  :  4.644  26.637    978
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.66 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 31.27 %
    Favored  : 64.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.29), residues: 888
  helix:  1.03 (0.26), residues: 406
  sheet:  0.24 (0.62), residues: 76
  loop : -1.52 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 182 
 TYR   0.024   0.001   TYR B  79 
 PHE   0.015   0.002   PHE B  77 
 TRP   0.011   0.001   TRP G   5 
 HIS   0.013   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7564)
  covalent geometry    : angle       0.69018 (10220)
  hydrogen bonds       : bond        0.04009 (  318)
  hydrogen bonds       : angle       4.48417 (  957)

*********************** 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
  279 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 242
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4587 (OUTLIER) cc_final: 0.3382 (mmt90)
REVERT: B   17 MET cc_start: 0.4978 (tpp) cc_final: 0.4672 (tpp)
REVERT: B   60 VAL cc_start: 0.8099 (p) cc_final: 0.7883 (p)
REVERT: B   74 CYS cc_start: 0.7661 (t) cc_final: 0.7093 (t)
REVERT: C   54 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6896 (mt-10)
REVERT: C  113 TRP cc_start: 0.8350 (p-90) cc_final: 0.7748 (p-90)
REVERT: C  149 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8320 (mtm180)
REVERT: G   70 TRP cc_start: 0.7286 (p90) cc_final: 0.7034 (p90)
REVERT: G   97 GLN cc_start: 0.8589 (mp10) cc_final: 0.8065 (mm-40)
REVERT: G  107 ILE cc_start: 0.7778 (tt) cc_final: 0.7481 (tt)
REVERT: D   68 GLN cc_start: 0.7700 (pt0) cc_final: 0.7492 (tt0)
REVERT: D   69 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6582 (tm-30)
REVERT: D  102 ASN cc_start: 0.8535 (m-40) cc_final: 0.8257 (m-40)
REVERT: D  125 LYS cc_start: 0.8127 (mttm) cc_final: 0.7907 (mtmm)
REVERT: D  161 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8193 (mm)
REVERT: D  164 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7686 (mm-30)
REVERT: D  171 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6485 (mt-10)
REVERT: D  190 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7443 (tm-30)
REVERT: D  194 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7233 (mm-30)
REVERT: D  200 ASP cc_start: 0.8511 (t0) cc_final: 0.8225 (t0)
REVERT: D  208 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7890 (ttpt)
REVERT: D  224 PHE cc_start: 0.8589 (t80) cc_final: 0.8150 (t80)
REVERT: D  234 LEU cc_start: 0.8480 (mt) cc_final: 0.8160 (mt)
REVERT: D  258 ASN cc_start: 0.8398 (t0) cc_final: 0.8113 (t0)
REVERT: D  260 PHE cc_start: 0.7839 (m-10) cc_final: 0.7309 (m-80)
REVERT: D  265 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7744 (mtmm)
REVERT: D  274 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6589 (mmtt)
REVERT: D  279 MET cc_start: 0.8272 (tpp) cc_final: 0.7867 (tpp)
REVERT: D  283 LYS cc_start: 0.8173 (tptt) cc_final: 0.7793 (tptt)
REVERT: D  285 LEU cc_start: 0.8215 (tt) cc_final: 0.7882 (tp)
REVERT: D  302 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7534 (ttmm)
REVERT: D  326 GLU cc_start: 0.6776 (tt0) cc_final: 0.6435 (tp30)
REVERT: D  335 GLU cc_start: 0.7586 (tp30) cc_final: 0.7180 (tp30)
REVERT: D  344 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7429 (mm-40)
REVERT: D  373 TYR cc_start: 0.8292 (m-10) cc_final: 0.8001 (m-80)
REVERT: D  377 ASN cc_start: 0.8741 (t0) cc_final: 0.8176 (t0)
REVERT: D  398 SER cc_start: 0.8728 (m) cc_final: 0.8212 (t)
REVERT: D  401 LYS cc_start: 0.8280 (ttmm) cc_final: 0.8063 (tttm)
REVERT: D  408 ASN cc_start: 0.8525 (t0) cc_final: 0.8254 (t0)
REVERT: D  414 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8122 (mt)
REVERT: D  415 VAL cc_start: 0.8506 (m) cc_final: 0.8290 (p)
  outliers start: 37
  outliers final: 27
  residues processed: 261
  average time/residue: 0.1131
  time to fit residues: 37.4217
Evaluate side-chains
  272 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 241
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   86 SER
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   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
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 D residue   74 LYS
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain D residue  253 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
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  448 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0060
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7198

-------------------------------------------------------------------------------
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**
D  77 GLN
D 212 HIS
D 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.143086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118175 restraints weight = 12159.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.122413 restraints weight = 6483.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.125348 restraints weight = 4165.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127188 restraints weight = 3018.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128695 restraints weight = 2417.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.5164

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= 0.146
  Angle     :  0.699  11.176  10220  Z= 0.354
  Chirality :  0.044   0.182   1114
  Planarity :  0.005   0.064   1312
  Dihedral  :  4.626  25.671    978
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.77 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 31.51 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.29), residues: 888
  helix:  1.03 (0.26), residues: 406
  sheet:  0.31 (0.61), residues: 76
  loop : -1.53 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 182 
 TYR   0.024   0.002   TYR B  79 
 PHE   0.017   0.002   PHE D 243 
 TRP   0.011   0.001   TRP G   5 
 HIS   0.014   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7564)
  covalent geometry    : angle       0.69876 (10220)
  hydrogen bonds       : bond        0.03980 (  318)
  hydrogen bonds       : angle       4.47429 (  957)

********************** 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
  279 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 245
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4559 (OUTLIER) cc_final: 0.3384 (mmt90)
REVERT: B   17 MET cc_start: 0.4954 (tpp) cc_final: 0.4672 (tpp)
REVERT: B   60 VAL cc_start: 0.8078 (p) cc_final: 0.7874 (p)
REVERT: B   74 CYS cc_start: 0.7644 (t) cc_final: 0.7073 (t)
REVERT: C   54 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6898 (mt-10)
REVERT: C  147 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7581 (ttt90)
REVERT: C  149 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8295 (mtm180)
REVERT: C  154 GLU cc_start: 0.6964 (tp30) cc_final: 0.6563 (tp30)
REVERT: G   70 TRP cc_start: 0.7260 (p90) cc_final: 0.7001 (p90)
REVERT: G  107 ILE cc_start: 0.7758 (tt) cc_final: 0.7457 (tt)
REVERT: D  102 ASN cc_start: 0.8545 (m-40) cc_final: 0.8272 (m-40)
REVERT: D  125 LYS cc_start: 0.8132 (mttm) cc_final: 0.7927 (mtmm)
REVERT: D  133 ARG cc_start: 0.8240 (ptp90) cc_final: 0.7964 (ptt90)
REVERT: D  161 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (mm)
REVERT: D  164 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7679 (mm-30)
REVERT: D  171 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6536 (mt-10)
REVERT: D  190 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: D  194 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7199 (mm-30)
REVERT: D  200 ASP cc_start: 0.8525 (t0) cc_final: 0.8249 (t0)
REVERT: D  208 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8095 (ttpt)
REVERT: D  224 PHE cc_start: 0.8585 (t80) cc_final: 0.8186 (t80)
REVERT: D  234 LEU cc_start: 0.8486 (mt) cc_final: 0.8169 (mt)
REVERT: D  251 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6890 (mt-10)
REVERT: D  258 ASN cc_start: 0.8395 (t0) cc_final: 0.8115 (t0)
REVERT: D  260 PHE cc_start: 0.7857 (m-10) cc_final: 0.7326 (m-80)
REVERT: D  265 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7747 (mtmm)
REVERT: D  279 MET cc_start: 0.8281 (tpp) cc_final: 0.7868 (tpp)
REVERT: D  283 LYS cc_start: 0.8115 (tptt) cc_final: 0.7727 (tptt)
REVERT: D  285 LEU cc_start: 0.8189 (tt) cc_final: 0.7851 (tp)
REVERT: D  302 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7543 (ttmm)
REVERT: D  326 GLU cc_start: 0.6784 (tt0) cc_final: 0.6447 (tp30)
REVERT: D  335 GLU cc_start: 0.7575 (tp30) cc_final: 0.7179 (tp30)
REVERT: D  344 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7437 (mm-40)
REVERT: D  373 TYR cc_start: 0.8297 (m-10) cc_final: 0.8071 (m-80)
REVERT: D  374 PHE cc_start: 0.8664 (m-80) cc_final: 0.8274 (m-80)
REVERT: D  377 ASN cc_start: 0.8727 (t0) cc_final: 0.8171 (t0)
REVERT: D  398 SER cc_start: 0.8727 (m) cc_final: 0.8299 (t)
REVERT: D  401 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8055 (tttm)
REVERT: D  408 ASN cc_start: 0.8548 (t0) cc_final: 0.8213 (t0)
REVERT: D  414 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8130 (mt)
REVERT: D  415 VAL cc_start: 0.8504 (m) cc_final: 0.8296 (p)
REVERT: D  437 TYR cc_start: 0.6705 (t80) cc_final: 0.6298 (t80)
REVERT: D  441 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7566 (mmm-85)
  outliers start: 34
  outliers final: 27
  residues processed: 263
  average time/residue: 0.1177
  time to fit residues: 38.9800
Evaluate side-chains
  275 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 243
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   86 SER
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   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain G residue    7 VAL
Chi-restraints excluded: chain G residue   13 VAL
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 D residue   74 LYS
Chi-restraints excluded: chain D residue   75 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  163 TYR
Chi-restraints excluded: chain D residue  253 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
Chi-restraints excluded: chain D residue  401 LYS
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  448 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 17 optimal weight:    0.0170
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 77 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0670
   chunk 45 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0370
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.1034

-------------------------------------------------------------------------------
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**
D  73 GLN
D  77 GLN
D 212 HIS
D 231 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.145848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.120660 restraints weight = 12393.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124989 restraints weight = 6598.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.127996 restraints weight = 4228.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.130001 restraints weight = 3065.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.131261 restraints weight = 2436.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.5214

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= 0.128
  Angle     :  0.690  10.560  10220  Z= 0.349
  Chirality :  0.043   0.175   1114
  Planarity :  0.005   0.040   1312
  Dihedral  :  4.533  24.332    978
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.21 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 32.13 %
    Favored  : 64.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.29), residues: 888
  helix:  1.09 (0.27), residues: 402
  sheet:  0.39 (0.61), residues: 76
  loop : -1.45 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 182 
 TYR   0.012   0.001   TYR G 111 
 PHE   0.017   0.001   PHE D 243 
 TRP   0.013   0.001   TRP D 375 
 HIS   0.014   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7564)
  covalent geometry    : angle       0.69015 (10220)
  hydrogen bonds       : bond        0.03528 (  318)
  hydrogen bonds       : angle       4.36595 (  957)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1568.96 seconds
wall clock time: 27 minutes 48.49 seconds (1668.49 seconds total)