Starting phenix.real_space_refine
on Wed Mar 12 17:01:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iv1_60917/03_2025/9iv1_60917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iv1_60917/03_2025/9iv1_60917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iv1_60917/03_2025/9iv1_60917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iv1_60917/03_2025/9iv1_60917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iv1_60917/03_2025/9iv1_60917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iv1_60917/03_2025/9iv1_60917.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5293      2.51       5
     N    1405      2.21       5
     O    1536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8284
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "S"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1698
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 49
    Chain: "B"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2496
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 85
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 85
    Chain: "G"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 401
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "R"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1899
          Classifications: {'peptide': 255}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 5, 'TRANS': 249}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 51
    Chain: "A"
      Number of atoms: 1769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1769
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 75
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'DHT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.33, per 1000 atoms: 0.64
  Number of scatterers: 8284
  At special positions: 0
  Unit cell: (97.58, 115.62, 114.8, 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      50     16.00
     O    1536      8.00
     N    1405      7.00
     C    5293      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=1.72
    Simple disulfide: pdb=" SG  CYS R 632 " - pdb=" SG  CYS R 704 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 998.0 milliseconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2072

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 12 sheets defined
      31.7% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 4.039A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 567 through 591
      removed outlier: 3.709A  pdb=" N   GLY R 573 " --> pdb=" O   ILE R 569 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   CYS R 574 " --> pdb=" O   SER R 570 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL R 578 " --> pdb=" O   CYS R 574 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 600 through 622
      removed outlier: 4.899A  pdb=" N   ALA R 606 " --> pdb=" O   TYR R 602 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 629 through 659
      removed outlier: 3.679A  pdb=" N   PHE R 642 " --> pdb=" O   LEU R 638 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ALA R 646 " --> pdb=" O   PHE R 642 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 671 through 680
    Processing helix  chain 'R' and resid 681 through 692
    Processing helix  chain 'R' and resid 720 through 741
      removed outlier: 3.755A  pdb=" N   ILE R 724 " --> pdb=" O   ALA R 720 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 755 through 770
      Proline residue:  R 767  - end of helix
    Processing helix  chain 'R' and resid 772 through 777
      removed outlier: 3.723A  pdb=" N   PHE R 775 " --> pdb=" O   SER R 772 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 789 through 794
      removed outlier: 3.816A  pdb=" N   LEU R 794 " --> pdb=" O   MET R 790 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 797 through 807
    Processing helix  chain 'R' and resid 810 through 827
    Processing helix  chain 'A' and resid 13 through 38
      removed outlier: 3.697A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 58
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.628A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 295 through 303
      removed outlier: 3.577A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.012A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 350
      removed outlier: 4.367A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 370
      No H-bonds generated for 'chain 'A' and resid 368 through 370'
    Processing helix  chain 'A' and resid 371 through 391
      removed outlier: 3.745A  pdb=" N   ILE A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'S' and resid 18 through 21
      removed outlier: 3.712A  pdb=" N   LEU S  20 " --> pdb=" O   LEU S  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 58 through 60
      removed outlier: 3.695A  pdb=" N   TYR S  50 " --> pdb=" O   TYR S  59 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 128 through 129
      removed outlier: 4.006A  pdb=" N   VAL S 143 " --> pdb=" O   ILE S 204 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.702A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.735A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.865A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.822A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.258A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.053A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.764A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 278
      removed outlier: 5.752A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.622A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1026 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: 2.40

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1531
        1.33 -     1.45: 2268
        1.45 -     1.57: 4598
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8467
  Sorted by residual:
  bond pdb=" CA  ALA R 720 "
       pdb=" C   ALA R 720 "
    ideal  model  delta    sigma   weight residual
    1.522  1.435  0.086 1.25e-02 6.40e+03 4.77e+01
  bond pdb=" CA  ALA R 761 "
       pdb=" C   ALA R 761 "
    ideal  model  delta    sigma   weight residual
    1.524  1.441  0.083 1.24e-02 6.50e+03 4.51e+01
  bond pdb=" CA  TRP R 714 "
       pdb=" C   TRP R 714 "
    ideal  model  delta    sigma   weight residual
    1.530  1.460  0.070 1.14e-02 7.69e+03 3.79e+01
  bond pdb=" CA  LEU S 221 "
       pdb=" C   LEU S 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.451  0.072 1.23e-02 6.61e+03 3.47e+01
  bond pdb=" CA  SER R 742 "
       pdb=" C   SER R 742 "
    ideal  model  delta    sigma   weight residual
    1.525  1.461  0.064 1.11e-02 8.12e+03 3.28e+01
  ... (remaining 8462 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 11363
        2.99 -     5.97: 148
        5.97 -     8.96: 27
        8.96 -    11.95: 9
       11.95 -    14.94: 2
  Bond angle restraints: 11549
  Sorted by residual:
  angle pdb=" N   PHE R 716 "
        pdb=" CA  PHE R 716 "
        pdb=" C   PHE R 716 "
      ideal   model   delta    sigma   weight residual
     114.39   99.45   14.94 1.45e+00 4.76e-01 1.06e+02
  angle pdb=" C   TYR S 223 "
        pdb=" N   PRO S 224 "
        pdb=" CA  PRO S 224 "
      ideal   model   delta    sigma   weight residual
     119.56  111.22    8.34 1.02e+00 9.61e-01 6.69e+01
  angle pdb=" N   MET R 635 "
        pdb=" CA  MET R 635 "
        pdb=" C   MET R 635 "
      ideal   model   delta    sigma   weight residual
     112.87  103.07    9.80 1.20e+00 6.94e-01 6.67e+01
  angle pdb=" N   PHE R 755 "
        pdb=" CA  PHE R 755 "
        pdb=" C   PHE R 755 "
      ideal   model   delta    sigma   weight residual
     113.01  104.30    8.71 1.20e+00 6.94e-01 5.27e+01
  angle pdb=" N   LEU S 221 "
        pdb=" CA  LEU S 221 "
        pdb=" C   LEU S 221 "
      ideal   model   delta    sigma   weight residual
     108.73   96.93   11.80 1.63e+00 3.76e-01 5.24e+01
  ... (remaining 11544 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4324
       17.94 -    35.88: 498
       35.88 -    53.81: 120
       53.81 -    71.75: 22
       71.75 -    89.69: 5
  Dihedral angle restraints: 4969
    sinusoidal: 1757
      harmonic: 3212
  Sorted by residual:
  dihedral pdb=" CA  THR R 700 "
           pdb=" C   THR R 700 "
           pdb=" N   SER R 701 "
           pdb=" CA  SER R 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.56   25.44     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.64   42.36     1      1.00e+01 1.00e-02 2.51e+01
  dihedral pdb=" CA  GLY R 699 "
           pdb=" C   GLY R 699 "
           pdb=" N   THR R 700 "
           pdb=" CA  THR R 700 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.82   24.18     0      5.00e+00 4.00e-02 2.34e+01
  ... (remaining 4966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1308
       0.108 -    0.216: 42
       0.216 -    0.324: 4
       0.324 -    0.432: 2
       0.432 -    0.540: 1
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CA  TYR S 223 "
            pdb=" N   TYR S 223 "
            pdb=" C   TYR S 223 "
            pdb=" CB  TYR S 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.30e+00
  chirality pdb=" CB  THR R 700 "
            pdb=" CA  THR R 700 "
            pdb=" OG1 THR R 700 "
            pdb=" CG2 THR R 700 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.19    0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" C10 DHT R 901 "
            pdb=" C1  DHT R 901 "
            pdb=" C5  DHT R 901 "
            pdb=" C9  DHT R 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.97   -2.62   -0.35 2.00e-01 2.50e+01 3.12e+00
  ... (remaining 1354 not shown)

  Planarity restraints: 1457
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL S 214 "   -0.020 2.00e-02 2.50e+03   3.87e-02 1.50e+01
        pdb=" C   VAL S 214 "    0.067 2.00e-02 2.50e+03
        pdb=" O   VAL S 214 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   TYR S 215 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER S 144 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   SER S 144 "    0.043 2.00e-02 2.50e+03
        pdb=" O   SER S 144 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE S 145 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 630 "    0.041 5.00e-02 4.00e+02   6.18e-02 6.12e+00
        pdb=" N   PRO R 631 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO R 631 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 631 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1454 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 578
        2.73 -     3.27: 8273
        3.27 -     3.81: 14017
        3.81 -     4.36: 16675
        4.36 -     4.90: 28635
  Nonbonded interactions: 68178
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 205 "
            pdb=" N   GLY A 206 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" OH  TYR S  60 "
            pdb=" O   PHE S  68 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASN A 292 "
            pdb=" N   LYS A 293 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.273 3.040
  ... (remaining 68173 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.080
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:13.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
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      :  0.006   0.086   8467  Z= 0.418
  Angle     :  0.859  14.936  11549  Z= 0.504
  Chirality :  0.051   0.540   1357
  Planarity :  0.005   0.062   1457
  Dihedral  : 16.437  89.689   2891
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  7.50 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 25.24 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.26), residues: 1093
  helix:  0.03 (0.29), residues: 364
  sheet: -0.37 (0.33), residues: 269
  loop : -1.84 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 714 
 HIS   0.010   0.001   HIS S 220 
 PHE   0.012   0.001   PHE R 775 
 TYR   0.020   0.001   TYR S 223 
 ARG   0.009   0.001   ARG B 137 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 191
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
REVERT: S  215 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7529 (m-10)
REVERT: R  706 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7945 (tp)
REVERT: R  707 SER cc_start: 0.8257 (m) cc_final: 0.8025 (p)
REVERT: A  290 PHE cc_start: 0.7860 (m-10) cc_final: 0.7643 (m-10)
  outliers start: 39
  outliers final: 16
  residues processed: 212
  average time/residue: 0.8175
  time to fit residues: 189.2336
Evaluate side-chains
  198 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 180
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   82 GLN
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  215 TYR
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  706 LEU
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue  261 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    0.2980
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
S  82 GLN
S 182 ASN
S 219 GLN
B 110 ASN
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
G  59 ASN
** R 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 795 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.132083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.114528 restraints weight = 12357.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.07
r_work: 0.3434 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8467  Z= 0.267
  Angle     :  0.643   9.700  11549  Z= 0.334
  Chirality :  0.045   0.346   1357
  Planarity :  0.005   0.057   1457
  Dihedral  :  6.563  59.033   1269
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.78 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 20.73 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.26), residues: 1093
  helix:  0.36 (0.28), residues: 367
  sheet: -0.36 (0.32), residues: 271
  loop : -1.85 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 680 
 HIS   0.004   0.001   HIS S 220 
 PHE   0.013   0.002   PHE B 278 
 TYR   0.023   0.002   TYR S 223 
 ARG   0.007   0.001   ARG B 137 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 180
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: S  211 ASP cc_start: 0.8241 (m-30) cc_final: 0.7789 (m-30)
REVERT: S  221 LEU cc_start: 0.7140 (tp) cc_final: 0.6526 (tp)
REVERT: B  187 VAL cc_start: 0.7882 (t) cc_final: 0.7605 (p)
REVERT: B  314 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7768 (ptp-170)
REVERT: R  706 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7873 (tp)
REVERT: R  707 SER cc_start: 0.7908 (m) cc_final: 0.7597 (p)
REVERT: A   32 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8110 (ttmm)
REVERT: A   33 ASP cc_start: 0.7752 (t70) cc_final: 0.7530 (t0)
REVERT: A   34 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8299 (ttpt)
REVERT: A  386 MET cc_start: 0.8653 (ttp) cc_final: 0.8450 (ttm)
  outliers start: 43
  outliers final: 17
  residues processed: 204
  average time/residue: 0.8224
  time to fit residues: 183.4930
Evaluate side-chains
  192 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  578 VAL
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  706 LEU
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 99 optimal weight:    8.9990
   chunk 106 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** S  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN
S 219 GLN
B 110 ASN
B 230 ASN
R 600 GLN
R 640 HIS
R 795 ASN
A 220 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.115025 restraints weight = 12543.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.09
r_work: 0.3441 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8467  Z= 0.210
  Angle     :  0.607   9.702  11549  Z= 0.311
  Chirality :  0.045   0.491   1357
  Planarity :  0.004   0.048   1457
  Dihedral  :  5.822  59.887   1252
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 22.87 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.26), residues: 1093
  helix:  0.68 (0.28), residues: 365
  sheet: -0.52 (0.32), residues: 276
  loop : -1.64 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.019   0.001   PHE S 200 
 TYR   0.019   0.001   TYR S 223 
 ARG   0.008   0.001   ARG B 137 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 0.941 
Fit side-chains
REVERT: S  117 LEU cc_start: 0.7121 (tp) cc_final: 0.6902 (tm)
REVERT: S  211 ASP cc_start: 0.8282 (m-30) cc_final: 0.7853 (m-30)
REVERT: B  101 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8263 (mtm)
REVERT: B  314 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7718 (ptp-170)
REVERT: R  706 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7911 (tp)
REVERT: R  707 SER cc_start: 0.8003 (m) cc_final: 0.7684 (p)
REVERT: R  713 ILE cc_start: 0.8149 (tp) cc_final: 0.7920 (tt)
REVERT: A   33 ASP cc_start: 0.7789 (t70) cc_final: 0.7518 (t0)
REVERT: A   34 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8333 (ttpt)
REVERT: A  209 GLU cc_start: 0.6902 (pp20) cc_final: 0.6624 (pp20)
REVERT: A  290 PHE cc_start: 0.7767 (m-10) cc_final: 0.7510 (m-10)
REVERT: A  386 MET cc_start: 0.8640 (ttp) cc_final: 0.8436 (ttm)
  outliers start: 40
  outliers final: 23
  residues processed: 208
  average time/residue: 0.7994
  time to fit residues: 181.8723
Evaluate side-chains
  206 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  706 LEU
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 102 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
S  35 HIS
S 182 ASN
B 110 ASN
B 155 ASN
B 230 ASN
R 600 GLN
R 795 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.128712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.111175 restraints weight = 12473.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.06
r_work: 0.3387 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   8467  Z= 0.419
  Angle     :  0.683   9.707  11549  Z= 0.355
  Chirality :  0.047   0.331   1357
  Planarity :  0.005   0.050   1457
  Dihedral  :  6.158  58.773   1252
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.60 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 22.75 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.26), residues: 1093
  helix:  0.41 (0.28), residues: 368
  sheet: -0.70 (0.32), residues: 278
  loop : -1.69 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.023   0.002   PHE B 278 
 TYR   0.023   0.002   TYR S 223 
 ARG   0.008   0.001   ARG B 137 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 193
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: S  211 ASP cc_start: 0.8299 (m-30) cc_final: 0.7897 (m-30)
REVERT: B  101 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8328 (mtm)
REVERT: B  205 ASP cc_start: 0.7617 (t0) cc_final: 0.7417 (t0)
REVERT: B  314 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7698 (ptp-170)
REVERT: R  594 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.7106 (t)
REVERT: R  706 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7988 (tp)
REVERT: R  707 SER cc_start: 0.8191 (m) cc_final: 0.7853 (p)
REVERT: R  713 ILE cc_start: 0.8296 (tp) cc_final: 0.8036 (tt)
REVERT: A   33 ASP cc_start: 0.7832 (t70) cc_final: 0.7561 (t0)
REVERT: A   34 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8311 (ttpt)
  outliers start: 48
  outliers final: 29
  residues processed: 220
  average time/residue: 0.7251
  time to fit residues: 175.4652
Evaluate side-chains
  218 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  176 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  578 VAL
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  706 LEU
Chi-restraints excluded: chain R residue  732 ILE
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0370
   chunk 6 optimal weight:    0.3980
   chunk 93 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** S  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN
B 110 ASN
B 155 ASN
B 225 HIS
B 230 ASN
B 259 GLN
R 600 GLN
R 795 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.132051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.114639 restraints weight = 12452.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.07
r_work: 0.3441 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8467  Z= 0.196
  Angle     :  0.614   8.602  11549  Z= 0.312
  Chirality :  0.042   0.251   1357
  Planarity :  0.004   0.049   1457
  Dihedral  :  5.818  57.484   1250
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 22.75 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.26), residues: 1093
  helix:  0.67 (0.28), residues: 367
  sheet: -0.56 (0.32), residues: 270
  loop : -1.65 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.013   0.001   PHE S 200 
 TYR   0.019   0.001   TYR S 178 
 ARG   0.008   0.001   ARG B 137 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 179
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: S   60 TYR cc_start: 0.8001 (m-80) cc_final: 0.7598 (m-80)
REVERT: S  211 ASP cc_start: 0.8272 (m-30) cc_final: 0.7896 (m-30)
REVERT: S  219 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7044 (pp30)
REVERT: B  205 ASP cc_start: 0.7525 (t0) cc_final: 0.7263 (t0)
REVERT: B  314 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7771 (ptp-170)
REVERT: R  623 PHE cc_start: 0.8200 (t80) cc_final: 0.7940 (t80)
REVERT: R  647 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8091 (m-10)
REVERT: R  706 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7912 (tp)
REVERT: R  707 SER cc_start: 0.8139 (m) cc_final: 0.7816 (p)
REVERT: R  713 ILE cc_start: 0.8194 (tp) cc_final: 0.7983 (tt)
REVERT: A   33 ASP cc_start: 0.7875 (t70) cc_final: 0.7572 (t0)
  outliers start: 54
  outliers final: 26
  residues processed: 210
  average time/residue: 0.8321
  time to fit residues: 189.9876
Evaluate side-chains
  205 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 175
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  578 VAL
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  647 PHE
Chi-restraints excluded: chain R residue  706 LEU
Chi-restraints excluded: chain R residue  722 PHE
Chi-restraints excluded: chain R residue  732 ILE
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 106 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** S  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN
B 110 ASN
B 155 ASN
B 230 ASN
B 259 GLN
R 600 GLN
R 795 ASN
A 220 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.132193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.114667 restraints weight = 12404.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.07
r_work: 0.3437 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8467  Z= 0.210
  Angle     :  0.604   9.455  11549  Z= 0.309
  Chirality :  0.042   0.248   1357
  Planarity :  0.004   0.048   1457
  Dihedral  :  5.710  57.392   1250
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 23.82 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.26), residues: 1093
  helix:  0.77 (0.28), residues: 367
  sheet: -0.49 (0.32), residues: 280
  loop : -1.65 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.012   0.001   PHE S 200 
 TYR   0.017   0.001   TYR S 223 
 ARG   0.007   0.000   ARG B 137 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 181
  time to evaluate  : 0.801 
Fit side-chains
REVERT: S   60 TYR cc_start: 0.8028 (m-80) cc_final: 0.7627 (m-80)
REVERT: S  211 ASP cc_start: 0.8299 (m-30) cc_final: 0.7885 (m-30)
REVERT: S  219 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6990 (pt0)
REVERT: B  205 ASP cc_start: 0.7417 (t0) cc_final: 0.7168 (t0)
REVERT: B  277 SER cc_start: 0.8271 (p) cc_final: 0.8066 (t)
REVERT: B  314 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7794 (ptp-170)
REVERT: R  623 PHE cc_start: 0.8115 (t80) cc_final: 0.7843 (t80)
REVERT: R  706 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7930 (tp)
REVERT: R  707 SER cc_start: 0.8156 (m) cc_final: 0.7887 (p)
REVERT: R  713 ILE cc_start: 0.8256 (tp) cc_final: 0.8027 (tt)
REVERT: A   33 ASP cc_start: 0.7907 (t70) cc_final: 0.7600 (t0)
REVERT: A  209 GLU cc_start: 0.6965 (pp20) cc_final: 0.6597 (pp20)
  outliers start: 46
  outliers final: 29
  residues processed: 207
  average time/residue: 0.9491
  time to fit residues: 212.6417
Evaluate side-chains
  208 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  176 LEU
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  578 VAL
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  642 PHE
Chi-restraints excluded: chain R residue  706 LEU
Chi-restraints excluded: chain R residue  722 PHE
Chi-restraints excluded: chain R residue  732 ILE
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 79 optimal weight:    0.0980
   chunk 81 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 51 optimal weight:    0.2980
   chunk 105 optimal weight:    8.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
S  35 HIS
S 182 ASN
B 110 ASN
B 155 ASN
B 225 HIS
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 795 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.129897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.112331 restraints weight = 12462.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.06
r_work: 0.3400 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8467  Z= 0.343
  Angle     :  0.666   9.818  11549  Z= 0.342
  Chirality :  0.045   0.283   1357
  Planarity :  0.005   0.050   1457
  Dihedral  :  5.937  55.148   1250
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.51 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 25.36 %
    Favored  : 69.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.26), residues: 1093
  helix:  0.64 (0.28), residues: 361
  sheet: -0.51 (0.32), residues: 282
  loop : -1.73 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.018   0.002   PHE B 278 
 TYR   0.020   0.002   TYR S 223 
 ARG   0.009   0.001   ARG B  49 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 189
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: S  117 LEU cc_start: 0.7366 (tp) cc_final: 0.7085 (tp)
REVERT: S  211 ASP cc_start: 0.8340 (m-30) cc_final: 0.7940 (m-30)
REVERT: S  219 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6954 (pt0)
REVERT: B  205 ASP cc_start: 0.7552 (t0) cc_final: 0.7253 (t0)
REVERT: B  314 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7757 (ptp-170)
REVERT: R  623 PHE cc_start: 0.8233 (t80) cc_final: 0.7916 (t80)
REVERT: R  713 ILE cc_start: 0.8279 (tp) cc_final: 0.8003 (tt)
REVERT: A   33 ASP cc_start: 0.7900 (t70) cc_final: 0.7589 (t0)
REVERT: A  383 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7907 (mp)
  outliers start: 43
  outliers final: 28
  residues processed: 215
  average time/residue: 0.9477
  time to fit residues: 221.9113
Evaluate side-chains
  215 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 184
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  176 LEU
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  578 VAL
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  732 ILE
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** S  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN
B 110 ASN
B 155 ASN
B 225 HIS
R 795 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.130812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.113282 restraints weight = 12562.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.08
r_work: 0.3419 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8467  Z= 0.254
  Angle     :  0.634  10.407  11549  Z= 0.325
  Chirality :  0.043   0.261   1357
  Planarity :  0.004   0.049   1457
  Dihedral  :  5.573  53.744   1248
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.05 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 26.07 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.26), residues: 1093
  helix:  0.77 (0.28), residues: 361
  sheet: -0.52 (0.32), residues: 282
  loop : -1.70 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.002   PHE S 200 
 TYR   0.021   0.002   TYR B 124 
 ARG   0.009   0.001   ARG B 137 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 180
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
REVERT: S   59 TYR cc_start: 0.8622 (m-80) cc_final: 0.8374 (m-10)
REVERT: S  117 LEU cc_start: 0.7305 (tp) cc_final: 0.7050 (tp)
REVERT: S  211 ASP cc_start: 0.8305 (m-30) cc_final: 0.7926 (m-30)
REVERT: S  219 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6910 (pt0)
REVERT: B  205 ASP cc_start: 0.7493 (t0) cc_final: 0.7196 (t0)
REVERT: B  314 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7801 (ptp-170)
REVERT: R  623 PHE cc_start: 0.8158 (t80) cc_final: 0.7835 (t80)
REVERT: A   33 ASP cc_start: 0.7923 (t70) cc_final: 0.7618 (t0)
REVERT: A  383 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7880 (mp)
REVERT: A  393 LEU cc_start: 0.8314 (mt) cc_final: 0.8081 (mt)
  outliers start: 40
  outliers final: 29
  residues processed: 205
  average time/residue: 1.0647
  time to fit residues: 240.4353
Evaluate side-chains
  209 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 177
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  176 LEU
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  642 PHE
Chi-restraints excluded: chain R residue  732 ILE
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 93 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** S  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN
B 110 ASN
B 155 ASN
B 225 HIS
G   5 ASN
R 795 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.130819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.113259 restraints weight = 12565.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.09
r_work: 0.3417 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8467  Z= 0.273
  Angle     :  0.643  10.780  11549  Z= 0.329
  Chirality :  0.044   0.255   1357
  Planarity :  0.004   0.049   1457
  Dihedral  :  5.543  52.442   1248
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.14 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 26.54 %
    Favored  : 68.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.26), residues: 1093
  helix:  0.78 (0.28), residues: 361
  sheet: -0.56 (0.32), residues: 282
  loop : -1.72 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.016   0.002   PHE S 200 
 TYR   0.020   0.002   TYR B 124 
 ARG   0.011   0.001   ARG B  49 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 184
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   59 TYR cc_start: 0.8633 (m-80) cc_final: 0.8378 (m-10)
REVERT: S  117 LEU cc_start: 0.7318 (tp) cc_final: 0.7068 (tp)
REVERT: S  211 ASP cc_start: 0.8316 (m-30) cc_final: 0.7918 (m-30)
REVERT: S  219 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6914 (pt0)
REVERT: B  205 ASP cc_start: 0.7496 (t0) cc_final: 0.7189 (t0)
REVERT: B  314 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7771 (ptp-170)
REVERT: R  578 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7777 (t)
REVERT: R  623 PHE cc_start: 0.8165 (t80) cc_final: 0.7826 (t80)
REVERT: A   33 ASP cc_start: 0.7893 (t70) cc_final: 0.7581 (t0)
REVERT: A  383 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7881 (mp)
REVERT: A  393 LEU cc_start: 0.8300 (mt) cc_final: 0.8066 (mt)
  outliers start: 40
  outliers final: 31
  residues processed: 207
  average time/residue: 0.8215
  time to fit residues: 185.7266
Evaluate side-chains
  216 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 181
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  176 LEU
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  578 VAL
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  642 PHE
Chi-restraints excluded: chain R residue  732 ILE
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0040
   chunk 74 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
** S  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN
B 110 ASN
B 155 ASN
B 225 HIS
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 795 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.131665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.114223 restraints weight = 12408.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.07
r_work: 0.3428 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8467  Z= 0.227
  Angle     :  0.632  11.738  11549  Z= 0.322
  Chirality :  0.043   0.240   1357
  Planarity :  0.004   0.049   1457
  Dihedral  :  5.398  50.844   1248
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.05 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 27.96 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.26), residues: 1093
  helix:  0.91 (0.28), residues: 361
  sheet: -0.58 (0.32), residues: 281
  loop : -1.68 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.002   PHE S 200 
 TYR   0.020   0.002   TYR B 124 
 ARG   0.010   0.001   ARG B  49 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 186
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   59 TYR cc_start: 0.8602 (m-80) cc_final: 0.8371 (m-10)
REVERT: S  211 ASP cc_start: 0.8321 (m-30) cc_final: 0.7912 (m-30)
REVERT: S  219 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6953 (pt0)
REVERT: B  205 ASP cc_start: 0.7473 (t0) cc_final: 0.7167 (t0)
REVERT: B  314 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7781 (ptp-170)
REVERT: R  578 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7710 (t)
REVERT: R  623 PHE cc_start: 0.8140 (t80) cc_final: 0.7808 (t80)
REVERT: A   33 ASP cc_start: 0.7877 (t70) cc_final: 0.7528 (t0)
REVERT: A  393 LEU cc_start: 0.8254 (mt) cc_final: 0.8005 (mt)
  outliers start: 36
  outliers final: 27
  residues processed: 205
  average time/residue: 0.8055
  time to fit residues: 180.1700
Evaluate side-chains
  209 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  176 LEU
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  567 SER
Chi-restraints excluded: chain R residue  578 VAL
Chi-restraints excluded: chain R residue  617 VAL
Chi-restraints excluded: chain R residue  732 ILE
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  778 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain A residue  383 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    8.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** S  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN
B 110 ASN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 225 HIS
R 795 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.132115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.114633 restraints weight = 12489.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.08
r_work: 0.3438 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8467  Z= 0.226
  Angle     :  0.655  13.899  11549  Z= 0.326
  Chirality :  0.044   0.232   1357
  Planarity :  0.004   0.049   1457
  Dihedral  :  5.359  50.099   1248
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.87 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 28.08 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.26), residues: 1093
  helix:  0.96 (0.28), residues: 361
  sheet: -0.57 (0.32), residues: 281
  loop : -1.68 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.002   PHE S 200 
 TYR   0.019   0.002   TYR B 124 
 ARG   0.009   0.001   ARG B 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6782.32 seconds
wall clock time: 118 minutes 18.86 seconds (7098.86 seconds total)