Starting phenix.real_space_refine
on Tue Feb  3 21:44:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8szk_40919/02_2026/8szk_40919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8szk_40919/02_2026/8szk_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_40919/02_2026/8szk_40919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8szk_40919/02_2026/8szk_40919.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8szk_40919/02_2026/8szk_40919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8szk_40919/02_2026/8szk_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-2.0-5952/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: 1.70, per 1000 atoms: 0.23
  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: 0.60
  Conformation dependent library (CDL) restraints added in 264.6 milliseconds
  

  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: 0.19
  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: 1.02

  Time building geometry restraints manager: 0.76 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:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.500
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.420
-------------------------------------------------------------------------------
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 are 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  : 0.248 
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: 0.8131 (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: 0.7795 (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  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: 0.1096
  time to fit residues: 39.7298
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  : 0.340 
-------------------------------------------------------------------------------
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
G  28 HIS
G  43 HIS
G  73 HIS
G 108 HIS
** D  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  73 GLN
D  77 GLN
D 212 HIS
D 228 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.147929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.122171 restraints weight = 12476.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.126433 restraints weight = 6844.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.129375 restraints weight = 4476.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131432 restraints weight = 3286.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.132743 restraints weight = 2625.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7564  Z= 0.196
  Angle     :  0.745   8.014  10220  Z= 0.392
  Chirality :  0.046   0.240   1114
  Planarity :  0.005   0.043   1312
  Dihedral  :  4.893  30.667    981
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.32 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 28.04 %
    Favored  : 66.63 %
  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 are not related in a simple way.
  whole: -0.34 (0.28), residues: 888
  helix:  0.79 (0.26), residues: 409
  sheet:  0.56 (0.53), residues: 88
  loop : -1.53 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A   9 
 TYR   0.021   0.002   TYR B  79 
 PHE   0.023   0.002   PHE G 112 
 TRP   0.028   0.002   TRP G   5 
 HIS   0.012   0.002   HIS G  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 7564)
  covalent geometry    : angle       0.74487 (10220)
  hydrogen bonds       : bond        0.06391 (  318)
  hydrogen bonds       : angle       5.28724 (  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
  308 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 265
  time to evaluate  : 0.175 
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: A    9 ARG cc_start: 0.6262 (ptm160) cc_final: 0.5884 (tmm-80)
REVERT: A   10 HIS cc_start: 0.6939 (m-70) cc_final: 0.5858 (m-70)
REVERT: B   30 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7608 (mt)
REVERT: C   54 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7056 (mt-10)
REVERT: C   91 GLU cc_start: 0.6676 (mp0) cc_final: 0.5828 (mp0)
REVERT: C  126 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5738 (mp0)
REVERT: C  144 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7307 (mm-30)
REVERT: G    5 TRP cc_start: 0.6932 (m-10) cc_final: 0.6697 (m-10)
REVERT: G    9 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7937 (mm)
REVERT: G  167 ARG cc_start: 0.7348 (ttp80) cc_final: 0.7138 (ttp80)
REVERT: D   68 GLN cc_start: 0.7684 (pt0) cc_final: 0.7331 (tt0)
REVERT: D  107 TYR cc_start: 0.7901 (t80) cc_final: 0.7685 (t80)
REVERT: D  115 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8092 (tp)
REVERT: D  118 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.8003 (t)
REVERT: D  126 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7606 (tpt)
REVERT: D  127 ILE cc_start: 0.8170 (mm) cc_final: 0.7931 (mt)
REVERT: D  161 LEU cc_start: 0.8422 (mm) cc_final: 0.8099 (mm)
REVERT: D  171 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6548 (mt-10)
REVERT: D  194 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7369 (mm-30)
REVERT: D  208 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7987 (ttpt)
REVERT: D  209 THR cc_start: 0.8377 (m) cc_final: 0.8120 (t)
REVERT: D  248 GLU cc_start: 0.7375 (mp0) cc_final: 0.6911 (mp0)
REVERT: D  256 ILE cc_start: 0.7065 (tt) cc_final: 0.6825 (tt)
REVERT: D  258 ASN cc_start: 0.8663 (t0) cc_final: 0.8435 (t0)
REVERT: D  265 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7808 (mtmm)
REVERT: D  274 LYS cc_start: 0.6901 (mmtt) cc_final: 0.6575 (mmtt)
REVERT: D  283 LYS cc_start: 0.8293 (tptt) cc_final: 0.7872 (tptt)
REVERT: D  285 LEU cc_start: 0.8236 (tt) cc_final: 0.7927 (tp)
REVERT: D  335 GLU cc_start: 0.7560 (tp30) cc_final: 0.7211 (tp30)
REVERT: D  344 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7185 (mm-40)
REVERT: D  348 ILE cc_start: 0.8272 (pt) cc_final: 0.8004 (pt)
REVERT: D  349 GLU cc_start: 0.7116 (mp0) cc_final: 0.6763 (mp0)
REVERT: D  355 GLN cc_start: 0.8206 (tp40) cc_final: 0.7793 (tp40)
REVERT: D  377 ASN cc_start: 0.8692 (t0) cc_final: 0.8363 (t0)
REVERT: D  385 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6639 (mm-30)
REVERT: D  398 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8717 (t)
REVERT: D  408 ASN cc_start: 0.8286 (t0) cc_final: 0.7784 (t0)
REVERT: D  444 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7424 (tm-30)
  outliers start: 43
  outliers final: 17
  residues processed: 288
  average time/residue: 0.1020
  time to fit residues: 37.0936
Evaluate side-chains
  282 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 257
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   32 GLU
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain 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    9 ILE
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  115 ILE
Chi-restraints excluded: chain D residue  118 SER
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  398 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    0.4980
   chunk 82 optimal weight:    0.0970
   chunk 52 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
C  63 ASN
G 139 HIS
G 146 GLN
D 212 HIS
D 387 ASN
D 406 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.148698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.123009 restraints weight = 12460.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.127330 restraints weight = 6807.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.130334 restraints weight = 4416.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.132453 restraints weight = 3219.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.133822 restraints weight = 2553.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7564  Z= 0.141
  Angle     :  0.659   7.790  10220  Z= 0.343
  Chirality :  0.044   0.268   1114
  Planarity :  0.004   0.036   1312
  Dihedral  :  4.577  29.023    978
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.64 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 29.65 %
    Favored  : 66.13 %
  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 are not related in a simple way.
  whole: -0.35 (0.28), residues: 888
  helix:  0.91 (0.26), residues: 413
  sheet:  0.34 (0.55), residues: 82
  loop : -1.64 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  83 
 TYR   0.016   0.002   TYR G 111 
 PHE   0.022   0.002   PHE A  15 
 TRP   0.013   0.001   TRP G   5 
 HIS   0.006   0.001   HIS D 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7564)
  covalent geometry    : angle       0.65851 (10220)
  hydrogen bonds       : bond        0.04909 (  318)
  hydrogen bonds       : angle       4.80367 (  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
  300 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 266
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4949 (mm-30)
REVERT: B   30 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7575 (mt)
REVERT: C   91 GLU cc_start: 0.6803 (mp0) cc_final: 0.5948 (mp0)
REVERT: C  126 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5691 (mp0)
REVERT: C  149 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7826 (mtm180)
REVERT: G    5 TRP cc_start: 0.7075 (m-10) cc_final: 0.6864 (m-10)
REVERT: G    7 VAL cc_start: 0.8611 (t) cc_final: 0.8362 (m)
REVERT: G   83 GLN cc_start: 0.8326 (mp10) cc_final: 0.7867 (mp10)
REVERT: D   68 GLN cc_start: 0.7739 (pt0) cc_final: 0.7373 (tt0)
REVERT: D   69 GLU cc_start: 0.6741 (tm-30) cc_final: 0.5968 (tm-30)
REVERT: D   73 GLN cc_start: 0.7967 (mt0) cc_final: 0.7372 (mt0)
REVERT: D  125 LYS cc_start: 0.8174 (mttm) cc_final: 0.7939 (mtmm)
REVERT: D  161 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8123 (mm)
REVERT: D  171 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6466 (mt-10)
REVERT: D  194 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7295 (mm-30)
REVERT: D  200 ASP cc_start: 0.8525 (t0) cc_final: 0.8247 (t0)
REVERT: D  208 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7631 (ttpt)
REVERT: D  248 GLU cc_start: 0.7344 (mp0) cc_final: 0.6365 (mp0)
REVERT: D  251 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7023 (mt-10)
REVERT: D  256 ILE cc_start: 0.7051 (tt) cc_final: 0.6800 (tt)
REVERT: D  258 ASN cc_start: 0.8593 (t0) cc_final: 0.8362 (t0)
REVERT: D  265 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7808 (mtmm)
REVERT: D  274 LYS cc_start: 0.6974 (mmtt) cc_final: 0.6610 (mmtt)
REVERT: D  283 LYS cc_start: 0.8300 (tptt) cc_final: 0.7850 (tptt)
REVERT: D  285 LEU cc_start: 0.8219 (tt) cc_final: 0.7807 (tp)
REVERT: D  335 GLU cc_start: 0.7547 (tp30) cc_final: 0.7302 (tp30)
REVERT: D  344 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7110 (mm-40)
REVERT: D  347 LYS cc_start: 0.7707 (mttp) cc_final: 0.7067 (mttp)
REVERT: D  355 GLN cc_start: 0.8218 (tp40) cc_final: 0.7772 (tp40)
REVERT: D  373 TYR cc_start: 0.8329 (m-10) cc_final: 0.8070 (m-80)
REVERT: D  385 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6535 (mm-30)
REVERT: D  408 ASN cc_start: 0.8471 (t0) cc_final: 0.8241 (t0)
  outliers start: 34
  outliers final: 18
  residues processed: 280
  average time/residue: 0.1057
  time to fit residues: 37.1465
Evaluate side-chains
  282 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 260
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   32 GLU
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   59 LEU
Chi-restraints excluded: chain G residue   65 VAL
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  174 ASP
Chi-restraints excluded: chain D residue  225 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:    2.9990
   chunk 3 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
D 212 HIS
D 289 HIS
D 387 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.147776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122235 restraints weight = 12617.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126582 restraints weight = 6729.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.129558 restraints weight = 4310.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.131607 restraints weight = 3121.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.132887 restraints weight = 2467.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7564  Z= 0.141
  Angle     :  0.641   8.739  10220  Z= 0.333
  Chirality :  0.044   0.211   1114
  Planarity :  0.005   0.054   1312
  Dihedral  :  4.491  24.532    978
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.21 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 28.29 %
    Favored  : 66.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.28), residues: 888
  helix:  0.97 (0.26), residues: 415
  sheet:  0.70 (0.60), residues: 72
  loop : -1.61 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A   9 
 TYR   0.018   0.002   TYR B  79 
 PHE   0.021   0.002   PHE A  15 
 TRP   0.016   0.002   TRP D 375 
 HIS   0.015   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7564)
  covalent geometry    : angle       0.64145 (10220)
  hydrogen bonds       : bond        0.04454 (  318)
  hydrogen bonds       : angle       4.58018 (  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
  294 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 251
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.6698 (tmm-80) cc_final: 0.6286 (tmm-80)
REVERT: C   91 GLU cc_start: 0.6770 (mp0) cc_final: 0.5890 (mp0)
REVERT: C  113 TRP cc_start: 0.8388 (p-90) cc_final: 0.7640 (p-90)
REVERT: C  126 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5747 (mp0)
REVERT: C  149 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7994 (mtm180)
REVERT: G    7 VAL cc_start: 0.8677 (t) cc_final: 0.8376 (m)
REVERT: G   97 GLN cc_start: 0.8492 (mp10) cc_final: 0.8094 (mm-40)
REVERT: D   68 GLN cc_start: 0.7779 (pt0) cc_final: 0.7411 (tt0)
REVERT: D  107 TYR cc_start: 0.7935 (t80) cc_final: 0.7587 (t80)
REVERT: D  115 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8018 (tp)
REVERT: D  125 LYS cc_start: 0.8149 (mttm) cc_final: 0.7947 (mtmm)
REVERT: D  161 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8186 (mm)
REVERT: D  171 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6414 (mt-10)
REVERT: D  194 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7317 (mm-30)
REVERT: D  208 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7821 (ttpt)
REVERT: D  248 GLU cc_start: 0.7331 (mp0) cc_final: 0.6483 (mp0)
REVERT: D  251 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6980 (mt-10)
REVERT: D  258 ASN cc_start: 0.8526 (t0) cc_final: 0.8283 (t0)
REVERT: D  265 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7824 (mtmm)
REVERT: D  274 LYS cc_start: 0.6949 (mmtt) cc_final: 0.6605 (mmtt)
REVERT: D  283 LYS cc_start: 0.8236 (tptt) cc_final: 0.7812 (tptt)
REVERT: D  285 LEU cc_start: 0.8195 (tt) cc_final: 0.7820 (tp)
REVERT: D  326 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6502 (tp30)
REVERT: D  335 GLU cc_start: 0.7607 (tp30) cc_final: 0.7274 (tp30)
REVERT: D  344 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7260 (mm-40)
REVERT: D  355 GLN cc_start: 0.8142 (tp40) cc_final: 0.7747 (tp40)
REVERT: D  373 TYR cc_start: 0.8289 (m-10) cc_final: 0.8019 (m-80)
REVERT: D  377 ASN cc_start: 0.8712 (t0) cc_final: 0.8334 (t0)
REVERT: D  385 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6447 (mm-30)
REVERT: D  398 SER cc_start: 0.8907 (m) cc_final: 0.8623 (t)
REVERT: D  408 ASN cc_start: 0.8434 (t0) cc_final: 0.8184 (t0)
  outliers start: 43
  outliers final: 24
  residues processed: 271
  average time/residue: 0.0896
  time to fit residues: 31.3332
Evaluate side-chains
  274 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 246
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain B residue   59 GLU
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   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain D residue  115 ILE
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  193 LEU
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  394 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
G 105 GLN
D 212 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.146643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120948 restraints weight = 12457.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.125279 restraints weight = 6747.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128251 restraints weight = 4370.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.130127 restraints weight = 3186.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.131660 restraints weight = 2558.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7564  Z= 0.147
  Angle     :  0.643  10.278  10220  Z= 0.329
  Chirality :  0.044   0.242   1114
  Planarity :  0.005   0.060   1312
  Dihedral  :  4.465  26.825    978
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.09 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 27.42 %
    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 are not related in a simple way.
  whole: -0.17 (0.28), residues: 888
  helix:  1.16 (0.26), residues: 406
  sheet:  0.90 (0.63), residues: 71
  loop : -1.68 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 370 
 TYR   0.023   0.002   TYR B  79 
 PHE   0.027   0.002   PHE D 396 
 TRP   0.019   0.001   TRP D 375 
 HIS   0.008   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7564)
  covalent geometry    : angle       0.64326 (10220)
  hydrogen bonds       : bond        0.04292 (  318)
  hydrogen bonds       : angle       4.47839 (  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
  294 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 243
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 TYR cc_start: 0.7391 (m-10) cc_final: 0.7158 (m-10)
REVERT: C   24 GLU cc_start: 0.6339 (tp30) cc_final: 0.6117 (tp30)
REVERT: C  113 TRP cc_start: 0.8379 (p-90) cc_final: 0.7713 (p-90)
REVERT: C  122 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6169 (tpp)
REVERT: C  126 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5819 (mp0)
REVERT: C  149 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8102 (mtm180)
REVERT: C  152 GLU cc_start: 0.6396 (mp0) cc_final: 0.5960 (mp0)
REVERT: G    7 VAL cc_start: 0.8598 (t) cc_final: 0.8263 (m)
REVERT: G   97 GLN cc_start: 0.8557 (mp10) cc_final: 0.8094 (mm-40)
REVERT: G  135 TYR cc_start: 0.7927 (t80) cc_final: 0.7583 (t80)
REVERT: G  139 HIS cc_start: 0.6848 (m-70) cc_final: 0.6322 (m90)
REVERT: D   68 GLN cc_start: 0.7813 (pt0) cc_final: 0.7439 (tt0)
REVERT: D   69 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6976 (tm-30)
REVERT: D   74 LYS cc_start: 0.8459 (mttm) cc_final: 0.8183 (tttm)
REVERT: D   77 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8260 (tm-30)
REVERT: D   78 CYS cc_start: 0.8217 (p) cc_final: 0.8014 (t)
REVERT: D  102 ASN cc_start: 0.8385 (m-40) cc_final: 0.8062 (m-40)
REVERT: D  115 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7990 (tp)
REVERT: D  125 LYS cc_start: 0.8171 (mttm) cc_final: 0.7953 (mtmm)
REVERT: D  161 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8189 (mm)
REVERT: D  171 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6446 (mt-10)
REVERT: D  194 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7320 (mm-30)
REVERT: D  208 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8059 (ttpt)
REVERT: D  234 LEU cc_start: 0.8381 (mt) cc_final: 0.8105 (mt)
REVERT: D  248 GLU cc_start: 0.7352 (mp0) cc_final: 0.6983 (mp0)
REVERT: D  258 ASN cc_start: 0.8465 (t0) cc_final: 0.8177 (t0)
REVERT: D  265 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7830 (mtmm)
REVERT: D  274 LYS cc_start: 0.6917 (mmtt) cc_final: 0.6546 (mmtt)
REVERT: D  279 MET cc_start: 0.8418 (tpp) cc_final: 0.7962 (tpp)
REVERT: D  283 LYS cc_start: 0.8226 (tptt) cc_final: 0.7808 (tptt)
REVERT: D  285 LEU cc_start: 0.8232 (tt) cc_final: 0.7871 (tp)
REVERT: D  326 GLU cc_start: 0.6858 (tt0) cc_final: 0.6528 (tp30)
REVERT: D  335 GLU cc_start: 0.7655 (tp30) cc_final: 0.7285 (tp30)
REVERT: D  344 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7279 (mm-40)
REVERT: D  355 GLN cc_start: 0.8144 (tp40) cc_final: 0.7757 (tp40)
REVERT: D  373 TYR cc_start: 0.8303 (m-10) cc_final: 0.8040 (m-80)
REVERT: D  377 ASN cc_start: 0.8712 (t0) cc_final: 0.8341 (t0)
REVERT: D  385 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6082 (mm-30)
REVERT: D  396 PHE cc_start: 0.8240 (t80) cc_final: 0.8010 (t80)
REVERT: D  398 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8476 (t)
REVERT: D  408 ASN cc_start: 0.8462 (t0) cc_final: 0.8191 (t0)
REVERT: D  425 MET cc_start: 0.6638 (mmm) cc_final: 0.6379 (mmm)
  outliers start: 51
  outliers final: 26
  residues processed: 269
  average time/residue: 0.0854
  time to fit residues: 29.6733
Evaluate side-chains
  271 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 239
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   24 VAL
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   99 ILE
Chi-restraints excluded: chain B residue  102 GLU
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  129 VAL
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  115 ILE
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  193 LEU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  394 ILE
Chi-restraints excluded: chain D residue  398 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0570
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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
G  56 HIS
D 212 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.146657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.121183 restraints weight = 12411.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.125535 restraints weight = 6690.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128510 restraints weight = 4314.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130366 restraints weight = 3134.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.131901 restraints weight = 2514.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.4211

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= 0.136
  Angle     :  0.639  11.111  10220  Z= 0.324
  Chirality :  0.044   0.299   1114
  Planarity :  0.004   0.052   1312
  Dihedral  :  4.413  26.438    978
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.32 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 30.40 %
    Favored  : 65.14 %
  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 are not related in a simple way.
  whole: -0.12 (0.28), residues: 888
  helix:  1.16 (0.26), residues: 405
  sheet:  0.93 (0.63), residues: 71
  loop : -1.60 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A   8 
 TYR   0.021   0.001   TYR B  79 
 PHE   0.014   0.002   PHE D 396 
 TRP   0.012   0.001   TRP D 375 
 HIS   0.008   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7564)
  covalent geometry    : angle       0.63943 (10220)
  hydrogen bonds       : bond        0.03990 (  318)
  hydrogen bonds       : angle       4.36233 (  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
  280 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 244
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4230 (OUTLIER) cc_final: 0.3042 (mmt90)
REVERT: B   60 VAL cc_start: 0.8288 (p) cc_final: 0.8064 (p)
REVERT: C   24 GLU cc_start: 0.6460 (tp30) cc_final: 0.6203 (tp30)
REVERT: C  113 TRP cc_start: 0.8381 (p-90) cc_final: 0.7738 (p-90)
REVERT: C  122 MET cc_start: 0.6663 (tpt) cc_final: 0.6128 (tpp)
REVERT: C  126 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5857 (mp0)
REVERT: C  149 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8154 (mtm180)
REVERT: C  152 GLU cc_start: 0.6490 (mp0) cc_final: 0.6050 (mp0)
REVERT: G    7 VAL cc_start: 0.8593 (t) cc_final: 0.8266 (m)
REVERT: G   44 TYR cc_start: 0.7699 (p90) cc_final: 0.7274 (p90)
REVERT: G   97 GLN cc_start: 0.8583 (mp10) cc_final: 0.8078 (mm-40)
REVERT: G  135 TYR cc_start: 0.7873 (t80) cc_final: 0.7502 (t80)
REVERT: G  139 HIS cc_start: 0.6873 (m-70) cc_final: 0.6302 (m90)
REVERT: D   68 GLN cc_start: 0.7826 (pt0) cc_final: 0.7442 (tt0)
REVERT: D   73 GLN cc_start: 0.7972 (mt0) cc_final: 0.7599 (mt0)
REVERT: D   74 LYS cc_start: 0.8513 (mttm) cc_final: 0.8113 (tttm)
REVERT: D  102 ASN cc_start: 0.8354 (m-40) cc_final: 0.8020 (m-40)
REVERT: D  161 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8159 (mm)
REVERT: D  164 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7667 (mm-30)
REVERT: D  171 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6411 (mt-10)
REVERT: D  194 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7281 (mm-30)
REVERT: D  208 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8059 (ttpt)
REVERT: D  224 PHE cc_start: 0.8342 (t80) cc_final: 0.7919 (t80)
REVERT: D  234 LEU cc_start: 0.8408 (mt) cc_final: 0.8047 (mt)
REVERT: D  248 GLU cc_start: 0.7347 (mp0) cc_final: 0.7052 (mp0)
REVERT: D  258 ASN cc_start: 0.8440 (t0) cc_final: 0.8159 (t0)
REVERT: D  265 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7732 (mtmm)
REVERT: D  274 LYS cc_start: 0.6900 (mmtt) cc_final: 0.6536 (mmtt)
REVERT: D  279 MET cc_start: 0.8379 (tpp) cc_final: 0.7932 (tpp)
REVERT: D  283 LYS cc_start: 0.8213 (tptt) cc_final: 0.7810 (tptt)
REVERT: D  285 LEU cc_start: 0.8229 (tt) cc_final: 0.7923 (tp)
REVERT: D  326 GLU cc_start: 0.6858 (tt0) cc_final: 0.6509 (tp30)
REVERT: D  335 GLU cc_start: 0.7615 (tp30) cc_final: 0.7204 (tp30)
REVERT: D  344 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7288 (mm-40)
REVERT: D  355 GLN cc_start: 0.8146 (tp40) cc_final: 0.7729 (tp40)
REVERT: D  373 TYR cc_start: 0.8295 (m-10) cc_final: 0.8011 (m-80)
REVERT: D  377 ASN cc_start: 0.8694 (t0) cc_final: 0.8311 (t0)
REVERT: D  396 PHE cc_start: 0.8178 (t80) cc_final: 0.7978 (t80)
REVERT: D  398 SER cc_start: 0.8870 (m) cc_final: 0.8621 (t)
REVERT: D  408 ASN cc_start: 0.8483 (t0) cc_final: 0.8183 (t0)
  outliers start: 36
  outliers final: 24
  residues processed: 264
  average time/residue: 0.0783
  time to fit residues: 26.5361
Evaluate side-chains
  268 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 241
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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 B residue   78 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain G residue   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  120 ILE
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain D residue   75 LEU
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  193 LEU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  306 LEU
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  349 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0980
   chunk 87 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 82 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0050
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   overall best weight:    0.2994

-------------------------------------------------------------------------------
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**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.147990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122460 restraints weight = 12431.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126849 restraints weight = 6701.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.129871 restraints weight = 4317.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.131951 restraints weight = 3135.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.133213 restraints weight = 2487.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7564  Z= 0.119
  Angle     :  0.640  12.467  10220  Z= 0.323
  Chirality :  0.044   0.327   1114
  Planarity :  0.005   0.070   1312
  Dihedral  :  4.329  25.672    978
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.53 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 29.78 %
    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 are not related in a simple way.
  whole: -0.09 (0.28), residues: 888
  helix:  1.17 (0.26), residues: 406
  sheet:  0.89 (0.62), residues: 71
  loop : -1.55 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 121 
 TYR   0.014   0.001   TYR G  44 
 PHE   0.018   0.001   PHE A  15 
 TRP   0.013   0.001   TRP D 375 
 HIS   0.005   0.001   HIS D 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7564)
  covalent geometry    : angle       0.64018 (10220)
  hydrogen bonds       : bond        0.03650 (  318)
  hydrogen bonds       : angle       4.28138 (  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
  279 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 247
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4170 (OUTLIER) cc_final: 0.3032 (mmt90)
REVERT: B   60 VAL cc_start: 0.8268 (p) cc_final: 0.8040 (p)
REVERT: C   24 GLU cc_start: 0.6353 (tp30) cc_final: 0.6084 (tp30)
REVERT: C   49 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7762 (mmm-85)
REVERT: C  113 TRP cc_start: 0.8346 (p-90) cc_final: 0.7697 (p-90)
REVERT: C  122 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6104 (tpp)
REVERT: C  126 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5864 (mp0)
REVERT: C  149 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8165 (mtm180)
REVERT: C  152 GLU cc_start: 0.6367 (mp0) cc_final: 0.6010 (mp0)
REVERT: G    7 VAL cc_start: 0.8450 (t) cc_final: 0.8144 (m)
REVERT: G  135 TYR cc_start: 0.7818 (t80) cc_final: 0.7512 (t80)
REVERT: G  139 HIS cc_start: 0.6832 (m-70) cc_final: 0.6420 (m90)
REVERT: D   68 GLN cc_start: 0.7845 (pt0) cc_final: 0.7437 (tt0)
REVERT: D   69 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6850 (tm-30)
REVERT: D   77 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8275 (tm-30)
REVERT: D  102 ASN cc_start: 0.8377 (m-40) cc_final: 0.8023 (m-40)
REVERT: D  161 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8156 (mm)
REVERT: D  171 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6443 (mt-10)
REVERT: D  172 SER cc_start: 0.8032 (t) cc_final: 0.7585 (p)
REVERT: D  194 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7244 (mm-30)
REVERT: D  208 LYS cc_start: 0.8387 (ttpt) cc_final: 0.7823 (ttpt)
REVERT: D  224 PHE cc_start: 0.8372 (t80) cc_final: 0.7919 (t80)
REVERT: D  234 LEU cc_start: 0.8410 (mt) cc_final: 0.8056 (mt)
REVERT: D  248 GLU cc_start: 0.7340 (mp0) cc_final: 0.6612 (mp0)
REVERT: D  251 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6982 (mt-10)
REVERT: D  258 ASN cc_start: 0.8408 (t0) cc_final: 0.8132 (t0)
REVERT: D  265 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7776 (mtmm)
REVERT: D  274 LYS cc_start: 0.6914 (mmtt) cc_final: 0.6514 (mmtt)
REVERT: D  279 MET cc_start: 0.8336 (tpp) cc_final: 0.7921 (tpp)
REVERT: D  283 LYS cc_start: 0.8189 (tptt) cc_final: 0.7833 (tptt)
REVERT: D  285 LEU cc_start: 0.8199 (tt) cc_final: 0.7894 (tp)
REVERT: D  302 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7456 (mtpp)
REVERT: D  320 LYS cc_start: 0.8160 (tppt) cc_final: 0.7473 (tppt)
REVERT: D  326 GLU cc_start: 0.6802 (tt0) cc_final: 0.6476 (tp30)
REVERT: D  335 GLU cc_start: 0.7573 (tp30) cc_final: 0.7183 (tp30)
REVERT: D  344 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7260 (mm-40)
REVERT: D  373 TYR cc_start: 0.8238 (m-10) cc_final: 0.8020 (m-80)
REVERT: D  377 ASN cc_start: 0.8612 (t0) cc_final: 0.8209 (t0)
REVERT: D  398 SER cc_start: 0.8850 (m) cc_final: 0.8590 (t)
REVERT: D  408 ASN cc_start: 0.8477 (t0) cc_final: 0.8193 (t0)
REVERT: D  414 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8027 (mt)
REVERT: D  441 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7611 (mmm160)
  outliers start: 32
  outliers final: 24
  residues processed: 263
  average time/residue: 0.0938
  time to fit residues: 31.3312
Evaluate side-chains
  272 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 242
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   17 PHE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  386 GLU
Chi-restraints excluded: chain D residue  414 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.144618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.119250 restraints weight = 12479.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.123582 restraints weight = 6696.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.126590 restraints weight = 4313.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.128653 restraints weight = 3120.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.130077 restraints weight = 2469.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.4600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7564  Z= 0.156
  Angle     :  0.662  11.941  10220  Z= 0.336
  Chirality :  0.045   0.350   1114
  Planarity :  0.005   0.055   1312
  Dihedral  :  4.359  24.965    978
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.88 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 28.66 %
    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 are not related in a simple way.
  whole: -0.22 (0.28), residues: 888
  helix:  0.99 (0.26), residues: 413
  sheet:  0.61 (0.58), residues: 81
  loop : -1.59 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 370 
 TYR   0.026   0.002   TYR B  79 
 PHE   0.024   0.002   PHE D 396 
 TRP   0.017   0.001   TRP G   5 
 HIS   0.013   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7564)
  covalent geometry    : angle       0.66214 (10220)
  hydrogen bonds       : bond        0.04162 (  318)
  hydrogen bonds       : angle       4.38836 (  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
  290 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 249
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.3997 (OUTLIER) cc_final: 0.2678 (mmt90)
REVERT: A   85 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6412 (t80)
REVERT: B   17 MET cc_start: 0.4590 (tpp) cc_final: 0.4328 (tpp)
REVERT: B   60 VAL cc_start: 0.8143 (p) cc_final: 0.7926 (p)
REVERT: C   49 ARG cc_start: 0.8081 (mmm-85) cc_final: 0.7834 (mmm-85)
REVERT: C   54 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6928 (mt-10)
REVERT: C  113 TRP cc_start: 0.8348 (p-90) cc_final: 0.7735 (p-90)
REVERT: C  122 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6268 (mmm)
REVERT: C  126 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5984 (mp0)
REVERT: C  149 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8216 (mtm180)
REVERT: G    7 VAL cc_start: 0.8453 (t) cc_final: 0.8164 (m)
REVERT: G   97 GLN cc_start: 0.8612 (mp10) cc_final: 0.8055 (mm-40)
REVERT: G  135 TYR cc_start: 0.7860 (t80) cc_final: 0.7571 (t80)
REVERT: D   68 GLN cc_start: 0.7878 (pt0) cc_final: 0.7496 (tt0)
REVERT: D   69 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6899 (tm-30)
REVERT: D  102 ASN cc_start: 0.8447 (m-40) cc_final: 0.8118 (m-40)
REVERT: D  161 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8173 (mm)
REVERT: D  164 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7660 (mm-30)
REVERT: D  171 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6442 (mt-10)
REVERT: D  194 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7320 (mm-30)
REVERT: D  208 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7853 (ttpt)
REVERT: D  224 PHE cc_start: 0.8458 (t80) cc_final: 0.8050 (t80)
REVERT: D  234 LEU cc_start: 0.8429 (mt) cc_final: 0.8084 (mt)
REVERT: D  251 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7064 (mt-10)
REVERT: D  258 ASN cc_start: 0.8403 (t0) cc_final: 0.8132 (t0)
REVERT: D  265 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7786 (mtmm)
REVERT: D  274 LYS cc_start: 0.6930 (mmtt) cc_final: 0.6519 (mmtt)
REVERT: D  279 MET cc_start: 0.8284 (tpp) cc_final: 0.7878 (tpp)
REVERT: D  283 LYS cc_start: 0.8210 (tptt) cc_final: 0.7848 (tptt)
REVERT: D  285 LEU cc_start: 0.8259 (tt) cc_final: 0.7944 (tp)
REVERT: D  302 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7469 (mtpp)
REVERT: D  326 GLU cc_start: 0.6847 (tt0) cc_final: 0.6512 (tp30)
REVERT: D  335 GLU cc_start: 0.7546 (tp30) cc_final: 0.7144 (tp30)
REVERT: D  344 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7340 (mm-40)
REVERT: D  355 GLN cc_start: 0.8168 (tp40) cc_final: 0.7744 (tp40)
REVERT: D  373 TYR cc_start: 0.8269 (m-10) cc_final: 0.8069 (m-80)
REVERT: D  377 ASN cc_start: 0.8584 (t0) cc_final: 0.8199 (t0)
REVERT: D  398 SER cc_start: 0.8772 (m) cc_final: 0.8367 (t)
REVERT: D  408 ASN cc_start: 0.8493 (t0) cc_final: 0.8070 (t0)
  outliers start: 41
  outliers final: 24
  residues processed: 271
  average time/residue: 0.1077
  time to fit residues: 37.0480
Evaluate side-chains
  277 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 247
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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   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   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  126 GLU
Chi-restraints excluded: chain G residue    2 GLU
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   80 HIS
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain G residue  129 VAL
Chi-restraints excluded: chain G residue  154 ILE
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  253 LEU
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  304 THR
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  349 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0060
   chunk 79 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 105 GLN
D 212 HIS
D 324 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.143006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.117914 restraints weight = 12241.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.122178 restraints weight = 6566.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.125122 restraints weight = 4233.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.127172 restraints weight = 3072.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128577 restraints weight = 2430.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7564  Z= 0.176
  Angle     :  0.702  12.531  10220  Z= 0.353
  Chirality :  0.046   0.383   1114
  Planarity :  0.005   0.039   1312
  Dihedral  :  4.463  26.558    978
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.43 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 30.40 %
    Favored  : 64.89 %
  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 are not related in a simple way.
  whole: -0.29 (0.28), residues: 888
  helix:  0.93 (0.26), residues: 412
  sheet:  0.59 (0.59), residues: 81
  loop : -1.62 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A   8 
 TYR   0.033   0.002   TYR B  79 
 PHE   0.022   0.002   PHE A  15 
 TRP   0.018   0.002   TRP G   5 
 HIS   0.012   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 7564)
  covalent geometry    : angle       0.70166 (10220)
  hydrogen bonds       : bond        0.04358 (  318)
  hydrogen bonds       : angle       4.43048 (  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
  289 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 251
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ARG cc_start: 0.4541 (OUTLIER) cc_final: 0.3286 (mmt90)
REVERT: B   17 MET cc_start: 0.4667 (tpp) cc_final: 0.4400 (tpp)
REVERT: B   60 VAL cc_start: 0.8147 (p) cc_final: 0.7931 (p)
REVERT: C   24 GLU cc_start: 0.6889 (tp30) cc_final: 0.6609 (tp30)
REVERT: C   54 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6889 (mt-10)
REVERT: C  113 TRP cc_start: 0.8328 (p-90) cc_final: 0.7749 (p-90)
REVERT: C  122 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6405 (tpt)
REVERT: C  149 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8263 (mtm180)
REVERT: G    7 VAL cc_start: 0.8452 (t) cc_final: 0.8161 (m)
REVERT: G  135 TYR cc_start: 0.7848 (t80) cc_final: 0.7469 (t80)
REVERT: D   68 GLN cc_start: 0.7877 (pt0) cc_final: 0.7572 (tt0)
REVERT: D   69 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: D   74 LYS cc_start: 0.8474 (tttm) cc_final: 0.8260 (tttm)
REVERT: D  102 ASN cc_start: 0.8517 (m-40) cc_final: 0.8158 (m-40)
REVERT: D  161 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: D  164 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7593 (mm-30)
REVERT: D  171 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6527 (mt-10)
REVERT: D  194 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7336 (mm-30)
REVERT: D  208 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7833 (ttpt)
REVERT: D  224 PHE cc_start: 0.8472 (t80) cc_final: 0.8114 (t80)
REVERT: D  231 ASN cc_start: 0.8034 (m-40) cc_final: 0.7806 (m110)
REVERT: D  234 LEU cc_start: 0.8468 (mt) cc_final: 0.8233 (mt)
REVERT: D  251 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7095 (mt-10)
REVERT: D  258 ASN cc_start: 0.8365 (t0) cc_final: 0.8127 (t0)
REVERT: D  265 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7760 (mtmm)
REVERT: D  274 LYS cc_start: 0.7051 (mmtt) cc_final: 0.6684 (mmtt)
REVERT: D  283 LYS cc_start: 0.8209 (tptt) cc_final: 0.7850 (tptt)
REVERT: D  285 LEU cc_start: 0.8283 (tt) cc_final: 0.7963 (tp)
REVERT: D  302 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7442 (mtpp)
REVERT: D  320 LYS cc_start: 0.8369 (tppt) cc_final: 0.7938 (mppt)
REVERT: D  326 GLU cc_start: 0.6915 (tt0) cc_final: 0.6596 (tp30)
REVERT: D  335 GLU cc_start: 0.7567 (tp30) cc_final: 0.7229 (tp30)
REVERT: D  344 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7445 (mm-40)
REVERT: D  377 ASN cc_start: 0.8575 (t0) cc_final: 0.8203 (t0)
REVERT: D  398 SER cc_start: 0.8743 (m) cc_final: 0.8287 (t)
REVERT: D  408 ASN cc_start: 0.8484 (t0) cc_final: 0.8146 (t0)
REVERT: D  414 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8115 (mt)
  outliers start: 38
  outliers final: 28
  residues processed: 271
  average time/residue: 0.1012
  time to fit residues: 34.7548
Evaluate side-chains
  280 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 247
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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   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   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 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 G residue  154 ILE
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  288 PHE
Chi-restraints excluded: chain D residue  304 THR
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  329 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  395 MET
Chi-restraints excluded: chain D residue  414 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 74 optimal weight:    0.0980
   chunk 13 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0970
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 HIS
D 387 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.145306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.120455 restraints weight = 12216.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.124795 restraints weight = 6512.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.127753 restraints weight = 4172.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.129653 restraints weight = 3020.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.131142 restraints weight = 2407.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.4991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7564  Z= 0.128
  Angle     :  0.679  12.494  10220  Z= 0.340
  Chirality :  0.044   0.384   1114
  Planarity :  0.005   0.046   1312
  Dihedral  :  4.401  25.079    978
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.09 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 32.13 %
    Favored  : 64.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.28), residues: 888
  helix:  0.94 (0.26), residues: 418
  sheet:  0.51 (0.62), residues: 76
  loop : -1.62 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  49 
 TYR   0.017   0.001   TYR B  79 
 PHE   0.017   0.001   PHE A  15 
 TRP   0.011   0.001   TRP C 110 
 HIS   0.014   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7564)
  covalent geometry    : angle       0.67924 (10220)
  hydrogen bonds       : bond        0.03629 (  318)
  hydrogen bonds       : angle       4.31299 (  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: 27
    poor density    : 252
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 PHE cc_start: 0.7287 (m-80) cc_final: 0.6842 (m-80)
REVERT: A   29 ARG cc_start: 0.4456 (OUTLIER) cc_final: 0.3289 (mmt90)
REVERT: B   17 MET cc_start: 0.4583 (tpp) cc_final: 0.4297 (tpp)
REVERT: B   60 VAL cc_start: 0.8057 (p) cc_final: 0.7842 (p)
REVERT: C   24 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6471 (tp30)
REVERT: C   54 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6854 (mt-10)
REVERT: C  113 TRP cc_start: 0.8298 (p-90) cc_final: 0.7707 (p-90)
REVERT: C  149 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8238 (mtm180)
REVERT: G    7 VAL cc_start: 0.8389 (t) cc_final: 0.8093 (m)
REVERT: G   70 TRP cc_start: 0.6524 (p90) cc_final: 0.6108 (p90)
REVERT: G  135 TYR cc_start: 0.7827 (t80) cc_final: 0.7445 (t80)
REVERT: G  139 HIS cc_start: 0.7011 (m-70) cc_final: 0.6615 (m-70)
REVERT: G  141 LYS cc_start: 0.7509 (ttpt) cc_final: 0.7294 (mtpt)
REVERT: D   68 GLN cc_start: 0.7854 (pt0) cc_final: 0.7563 (tt0)
REVERT: D   69 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6921 (tm-30)
REVERT: D   74 LYS cc_start: 0.8425 (tttm) cc_final: 0.8214 (tttm)
REVERT: D  102 ASN cc_start: 0.8505 (m-40) cc_final: 0.8153 (m-40)
REVERT: D  161 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8150 (mm)
REVERT: D  164 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7620 (mm-30)
REVERT: D  171 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6317 (mt-10)
REVERT: D  194 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7254 (mm-30)
REVERT: D  208 LYS cc_start: 0.8429 (ttpt) cc_final: 0.7881 (ttpt)
REVERT: D  224 PHE cc_start: 0.8461 (t80) cc_final: 0.8069 (t80)
REVERT: D  231 ASN cc_start: 0.8026 (m-40) cc_final: 0.7776 (m110)
REVERT: D  234 LEU cc_start: 0.8400 (mt) cc_final: 0.8149 (mt)
REVERT: D  251 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7044 (mt-10)
REVERT: D  258 ASN cc_start: 0.8351 (t0) cc_final: 0.8129 (t0)
REVERT: D  260 PHE cc_start: 0.7774 (m-10) cc_final: 0.7267 (m-80)
REVERT: D  265 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7689 (mtmm)
REVERT: D  274 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6566 (mmtt)
REVERT: D  279 MET cc_start: 0.8330 (tpp) cc_final: 0.7893 (tpp)
REVERT: D  283 LYS cc_start: 0.8171 (tptt) cc_final: 0.7840 (tptt)
REVERT: D  285 LEU cc_start: 0.8190 (tt) cc_final: 0.7881 (tp)
REVERT: D  302 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7619 (ttmm)
REVERT: D  303 ASP cc_start: 0.7811 (t0) cc_final: 0.7492 (t0)
REVERT: D  320 LYS cc_start: 0.8318 (tppt) cc_final: 0.7916 (mppt)
REVERT: D  326 GLU cc_start: 0.6888 (tt0) cc_final: 0.6546 (tp30)
REVERT: D  335 GLU cc_start: 0.7599 (tp30) cc_final: 0.7207 (tp30)
REVERT: D  344 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7297 (mm-40)
REVERT: D  355 GLN cc_start: 0.8127 (tp40) cc_final: 0.7717 (tp40)
REVERT: D  374 PHE cc_start: 0.8570 (m-80) cc_final: 0.8163 (m-80)
REVERT: D  377 ASN cc_start: 0.8554 (t0) cc_final: 0.8017 (t0)
REVERT: D  398 SER cc_start: 0.8745 (m) cc_final: 0.8314 (t)
REVERT: D  408 ASN cc_start: 0.8472 (t0) cc_final: 0.8125 (t0)
REVERT: D  414 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8080 (mt)
  outliers start: 27
  outliers final: 21
  residues processed: 267
  average time/residue: 0.0971
  time to fit residues: 32.8422
Evaluate side-chains
  274 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 248
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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   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   24 GLU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain G residue    2 GLU
Chi-restraints excluded: chain G residue   65 VAL
Chi-restraints excluded: chain G residue   80 HIS
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  114 CYS
Chi-restraints excluded: chain D residue   77 GLN
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  271 PHE
Chi-restraints excluded: chain D residue  304 THR
Chi-restraints excluded: chain D residue  329 PHE
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  414 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.143897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.118977 restraints weight = 12369.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.123339 restraints weight = 6596.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.126287 restraints weight = 4229.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.128353 restraints weight = 3057.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.129618 restraints weight = 2417.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.5087

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= 0.143
  Angle     :  0.689  12.806  10220  Z= 0.345
  Chirality :  0.046   0.443   1114
  Planarity :  0.005   0.043   1312
  Dihedral  :  4.416  26.287    978
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.32 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 32.01 %
    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 are not related in a simple way.
  whole: -0.23 (0.28), residues: 888
  helix:  1.01 (0.26), residues: 418
  sheet:  0.50 (0.62), residues: 76
  loop : -1.61 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 182 
 TYR   0.025   0.002   TYR B  79 
 PHE   0.020   0.002   PHE A  15 
 TRP   0.015   0.001   TRP G   5 
 HIS   0.014   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7564)
  covalent geometry    : angle       0.68851 (10220)
  hydrogen bonds       : bond        0.03752 (  318)
  hydrogen bonds       : angle       4.30551 (  957)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1328.87 seconds
wall clock time: 23 minutes 36.81 seconds (1416.81 seconds total)