Starting phenix.real_space_refine
on Wed Feb  4 19:18:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ykd_39365/02_2026/8ykd_39365.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ykd_39365/02_2026/8ykd_39365.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ykd_39365/02_2026/8ykd_39365.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ykd_39365/02_2026/8ykd_39365.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ykd_39365/02_2026/8ykd_39365.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ykd_39365/02_2026/8ykd_39365.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3724 atoms to isotropic.
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      60      5.16       5
     C    6016      2.51       5
     N    1590      2.21       5
     O    1744      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9410
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1850
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "B"
      Number of atoms: 2551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2551
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 33
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 950
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "R"
      Number of atoms: 1842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1842
          Classifications: {'peptide': 240}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 235}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 126
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 118
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 81
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'AND': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.24
  Number of scatterers: 9410
  At special positions: 0
  Unit cell: (92.4, 119.7, 122.85, 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      60     16.00
     O    1744      8.00
     N    1590      7.00
     C    6016      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.01
    Simple disulfide: pdb=" SG  CYS R 686 " - pdb=" SG  CYS R 770 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 390.3 milliseconds
  

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2280

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 15 sheets defined
      32.9% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 50
      removed outlier: 3.506A  pdb=" N   ALA A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 74
      removed outlier: 3.778A  pdb=" N   MET A  70 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 249
      removed outlier: 3.618A  pdb=" N   ASN A 249 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
      removed outlier: 3.501A  pdb=" N   ASN A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.198A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.725A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.579A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.607A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.752A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'R' and resid 620 through 645
      removed outlier: 3.808A  pdb=" N   PHE R 634 " --> pdb=" O   LEU R 630 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA R 644 " --> pdb=" O   VAL R 640 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 646 through 649
      removed outlier: 3.835A  pdb=" N   ARG R 649 " --> pdb=" O   GLU R 646 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 646 through 649'
    Processing helix  chain 'R' and resid 651 through 677
      removed outlier: 3.690A  pdb=" N   LYS R 655 " --> pdb=" O   ASP R 651 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 682 through 713
    Processing helix  chain 'R' and resid 725 through 749
      removed outlier: 3.586A  pdb=" N   ILE R 737 " --> pdb=" O   VAL R 733 " (cutoff:3.500A)
      Proline residue:  R 738  - end of helix
      removed outlier: 3.583A  pdb=" N   VAL R 741 " --> pdb=" O   ILE R 737 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 750 through 753
    Processing helix  chain 'R' and resid 782 through 809
      removed outlier: 3.572A  pdb=" N   LYS R 808 " --> pdb=" O   LEU R 804 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 824 through 835
      removed outlier: 3.628A  pdb=" N   LEU R 830 " --> pdb=" O   SER R 826 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 836 through 839
    Processing helix  chain 'R' and resid 840 through 845
    Processing helix  chain 'R' and resid 849 through 859
    Processing helix  chain 'R' and resid 862 through 872
    Processing helix  chain 'R' and resid 875 through 882
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.807A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.630A  pdb=" N   ASP S 223 " --> pdb=" O   GLU S 220 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 220 through 224'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224
      removed outlier: 3.596A  pdb=" N   VAL A 224 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL A 227 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ARG A  52 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   ILE A 255 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU A  54 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL A 257 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   VAL A 258 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.673A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.943A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.472A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.575A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.332A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.223A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.519A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.674A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.531A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.748A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.055A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.628A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    439 hydrogen bonds defined for protein.
    1230 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1799
        1.33 -     1.45: 2615
        1.45 -     1.58: 5118
        1.58 -     1.70: 0
        1.70 -     1.83: 85
  Bond restraints: 9617
  Sorted by residual:
  bond pdb=" N   PRO G  60 "
       pdb=" CA  PRO G  60 "
    ideal  model  delta    sigma   weight residual
    1.473  1.431  0.042 8.50e-03 1.38e+04 2.44e+01
  bond pdb=" CA  ASN G  59 "
       pdb=" C   ASN G  59 "
    ideal  model  delta    sigma   weight residual
    1.526  1.473  0.053 1.14e-02 7.69e+03 2.17e+01
  bond pdb=" C   ALA N  40 "
       pdb=" N   PRO N  41 "
    ideal  model  delta    sigma   weight residual
    1.332  1.376 -0.044 1.12e-02 7.97e+03 1.57e+01
  bond pdb=" C   ARG S 180 "
       pdb=" N   PRO S 181 "
    ideal  model  delta    sigma   weight residual
    1.334  1.392 -0.057 1.51e-02 4.39e+03 1.44e+01
  bond pdb=" CA  ARG B  46 "
       pdb=" C   ARG B  46 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.25e-02 6.40e+03 1.03e+01
  ... (remaining 9612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 12605
        2.91 -     5.82: 393
        5.82 -     8.73: 63
        8.73 -    11.64: 9
       11.64 -    14.55: 1
  Bond angle restraints: 13071
  Sorted by residual:
  angle pdb=" N   LEU R 620 "
        pdb=" CA  LEU R 620 "
        pdb=" C   LEU R 620 "
      ideal   model   delta    sigma   weight residual
     111.82  101.84    9.98 1.16e+00 7.43e-01 7.40e+01
  angle pdb=" C   PHE N 108 "
        pdb=" N   ASP N 109 "
        pdb=" CA  ASP N 109 "
      ideal   model   delta    sigma   weight residual
     122.46  132.25   -9.79 1.41e+00 5.03e-01 4.83e+01
  angle pdb=" C   ASN G  59 "
        pdb=" N   PRO G  60 "
        pdb=" CA  PRO G  60 "
      ideal   model   delta    sigma   weight residual
     121.04  113.69    7.35 1.21e+00 6.83e-01 3.69e+01
  angle pdb=" N   LEU S  86 "
        pdb=" CA  LEU S  86 "
        pdb=" C   LEU S  86 "
      ideal   model   delta    sigma   weight residual
     109.15  117.74   -8.59 1.44e+00 4.82e-01 3.56e+01
  angle pdb=" C   TYR S 235 "
        pdb=" N   PRO S 236 "
        pdb=" CA  PRO S 236 "
      ideal   model   delta    sigma   weight residual
     120.79  113.94    6.85 1.30e+00 5.92e-01 2.78e+01
  ... (remaining 13066 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 5184
       16.97 -    33.94: 383
       33.94 -    50.91: 83
       50.91 -    67.88: 12
       67.88 -    84.85: 10
  Dihedral angle restraints: 5672
    sinusoidal: 2129
      harmonic: 3543
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   32.88   60.12     1      1.00e+01 1.00e-02 4.82e+01
  dihedral pdb=" CA  PRO B 194 "
           pdb=" C   PRO B 194 "
           pdb=" N   ASP B 195 "
           pdb=" CA  ASP B 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.65   25.35     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  GLY S  54 "
           pdb=" C   GLY S  54 "
           pdb=" N   SER S  55 "
           pdb=" CA  SER S  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.19  -24.81     0      5.00e+00 4.00e-02 2.46e+01
  ... (remaining 5669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1279
       0.094 -    0.188: 194
       0.188 -    0.281: 15
       0.281 -    0.375: 6
       0.375 -    0.469: 2
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" CB  THR A 325 "
            pdb=" CA  THR A 325 "
            pdb=" OG1 THR A 325 "
            pdb=" CG2 THR A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.08    0.47 2.00e-01 2.50e+01 5.50e+00
  chirality pdb=" CB  ILE S 100 "
            pdb=" CA  ILE S 100 "
            pdb=" CG1 ILE S 100 "
            pdb=" CG2 ILE S 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.78e+00
  chirality pdb=" CB  VAL R 640 "
            pdb=" CA  VAL R 640 "
            pdb=" CG1 VAL R 640 "
            pdb=" CG2 VAL R 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.92e+00
  ... (remaining 1493 not shown)

  Planarity restraints: 1654
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET S 230 "    0.023 2.00e-02 2.50e+03   4.79e-02 2.30e+01
        pdb=" C   MET S 230 "   -0.083 2.00e-02 2.50e+03
        pdb=" O   MET S 230 "    0.032 2.00e-02 2.50e+03
        pdb=" N   GLN S 231 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR G  52 "    0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   THR G  52 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR G  52 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PRO G  53 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER S  85 "    0.015 2.00e-02 2.50e+03   3.10e-02 9.59e+00
        pdb=" C   SER S  85 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   SER S  85 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU S  86 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1651 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2159
        2.79 -     3.32: 8325
        3.32 -     3.84: 16430
        3.84 -     4.37: 19249
        4.37 -     4.90: 32782
  Nonbonded interactions: 78945
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  25 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   GLY S  33 "
            pdb=" OG  SER S  99 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.342 3.040
  ... (remaining 78940 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:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.390
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
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      :  0.007   0.077   9621  Z= 0.336
  Angle     :  1.280  51.475  13079  Z= 0.702
  Chirality :  0.070   0.469   1496
  Planarity :  0.010   0.095   1654
  Dihedral  : 13.108  84.854   3380
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.22 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.21), residues: 1205
  helix: -2.41 (0.20), residues: 357
  sheet: -1.09 (0.28), residues: 288
  loop : -1.86 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.002   ARG B  49 
 TYR   0.044   0.003   TYR B  85 
 PHE   0.045   0.004   PHE R 696 
 TRP   0.031   0.004   TRP A 244 
 HIS   0.018   0.004   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 ( 9617)
  covalent geometry    : angle       1.19835 (13071)
  SS BOND              : bond        0.01059 (    4)
  SS BOND              : angle      18.24756 (    8)
  hydrogen bonds       : bond        0.26126 (  434)
  hydrogen bonds       : angle       9.30931 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 307
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  225 ASP cc_start: 0.6881 (m-30) cc_final: 0.6652 (m-30)
REVERT: A  275 SER cc_start: 0.8165 (m) cc_final: 0.7867 (t)
REVERT: A  347 ARG cc_start: 0.8008 (ptp90) cc_final: 0.7665 (ptp90)
REVERT: A  389 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6720 (mtm110)
REVERT: B  173 THR cc_start: 0.8079 (p) cc_final: 0.7801 (p)
REVERT: B  221 THR cc_start: 0.7732 (m) cc_final: 0.7312 (m)
REVERT: B  228 ASP cc_start: 0.6757 (m-30) cc_final: 0.6504 (m-30)
REVERT: B  312 ASP cc_start: 0.7195 (m-30) cc_final: 0.6838 (m-30)
REVERT: B  322 ASP cc_start: 0.7195 (m-30) cc_final: 0.6961 (m-30)
REVERT: G   28 ILE cc_start: 0.7643 (pt) cc_final: 0.6797 (pt)
REVERT: N    6 GLU cc_start: 0.7431 (pm20) cc_final: 0.7028 (pm20)
REVERT: N   20 LEU cc_start: 0.8471 (mt) cc_final: 0.8227 (mt)
REVERT: N   60 TYR cc_start: 0.8090 (m-10) cc_final: 0.7739 (m-80)
REVERT: N  108 PHE cc_start: 0.6620 (m-80) cc_final: 0.6027 (m-80)
REVERT: R  723 ILE cc_start: 0.8676 (mm) cc_final: 0.8418 (mm)
REVERT: R  860 ASN cc_start: 0.6358 (m-40) cc_final: 0.6152 (m-40)
REVERT: R  868 PHE cc_start: 0.7165 (t80) cc_final: 0.6855 (t80)
REVERT: S   31 SER cc_start: 0.8000 (m) cc_final: 0.7690 (p)
REVERT: S   32 PHE cc_start: 0.8449 (m-80) cc_final: 0.8242 (m-80)
REVERT: S   86 LEU cc_start: 0.8883 (mp) cc_final: 0.8613 (mp)
REVERT: S  140 MET cc_start: 0.8591 (mmm) cc_final: 0.8210 (mmm)
REVERT: S  219 LEU cc_start: 0.7479 (tp) cc_final: 0.7272 (tt)
REVERT: S  231 GLN cc_start: 0.8150 (pp30) cc_final: 0.7616 (pp30)
REVERT: S  239 PHE cc_start: 0.7737 (m-80) cc_final: 0.6878 (m-80)
  outliers start: 3
  outliers final: 3
  residues processed: 310
  average time/residue: 0.4491
  time to fit residues: 150.7186
Evaluate side-chains
  253 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 250
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  120 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.3980
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
A 292 ASN
A 371 ASN
B  75 GLN
B 156 GLN
B 175 GLN
B 313 ASN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 659 GLN
R 849 ASN
R 863 GLN
S 232 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.110685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.100106 restraints weight = 16216.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.12
r_work: 0.3297 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9621  Z= 0.192
  Angle     :  0.657   9.116  13079  Z= 0.351
  Chirality :  0.044   0.227   1496
  Planarity :  0.006   0.072   1654
  Dihedral  :  5.028  29.822   1383
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.99 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.23), residues: 1205
  helix:  0.10 (0.26), residues: 358
  sheet: -0.92 (0.27), residues: 308
  loop : -1.42 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 314 
 TYR   0.021   0.002   TYR R 785 
 PHE   0.023   0.002   PHE R 832 
 TRP   0.029   0.002   TRP A 281 
 HIS   0.007   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 9617)
  covalent geometry    : angle       0.65646 (13071)
  SS BOND              : bond        0.00472 (    4)
  SS BOND              : angle       0.79505 (    8)
  hydrogen bonds       : bond        0.04642 (  434)
  hydrogen bonds       : angle       5.46563 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 275
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.8403 (mmt90) cc_final: 0.8107 (mmt-90)
REVERT: A   65 THR cc_start: 0.8549 (m) cc_final: 0.8147 (p)
REVERT: A  265 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7800 (mtp85)
REVERT: A  267 GLN cc_start: 0.8163 (tp40) cc_final: 0.7922 (mm-40)
REVERT: A  268 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: A  271 ASN cc_start: 0.7892 (m-40) cc_final: 0.7188 (m110)
REVERT: A  275 SER cc_start: 0.8684 (m) cc_final: 0.8453 (t)
REVERT: A  347 ARG cc_start: 0.8580 (ptp90) cc_final: 0.8295 (ptp90)
REVERT: B   17 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8399 (tt0)
REVERT: B   20 ASP cc_start: 0.7967 (m-30) cc_final: 0.7446 (m-30)
REVERT: B   46 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7689 (mpp80)
REVERT: B   75 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8438 (mm-40)
REVERT: B  101 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8361 (mtm)
REVERT: B  134 ARG cc_start: 0.8309 (pmm-80) cc_final: 0.7902 (ptp90)
REVERT: B  217 MET cc_start: 0.7947 (ppp) cc_final: 0.7476 (ppp)
REVERT: B  228 ASP cc_start: 0.7986 (m-30) cc_final: 0.7647 (m-30)
REVERT: B  259 GLN cc_start: 0.7804 (mp10) cc_final: 0.7354 (mp10)
REVERT: B  297 TRP cc_start: 0.8807 (m100) cc_final: 0.8598 (m100)
REVERT: B  314 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7673 (mtp180)
REVERT: G   62 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7325 (tmm-80)
REVERT: N    6 GLU cc_start: 0.7936 (pm20) cc_final: 0.7631 (pm20)
REVERT: N   60 TYR cc_start: 0.8626 (m-10) cc_final: 0.8098 (m-80)
REVERT: N  113 THR cc_start: 0.8522 (m) cc_final: 0.8266 (p)
REVERT: R  623 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7742 (pt)
REVERT: R  641 THR cc_start: 0.8544 (m) cc_final: 0.8300 (p)
REVERT: R  643 ILE cc_start: 0.8568 (mt) cc_final: 0.8233 (mp)
REVERT: R  691 VAL cc_start: 0.8156 (m) cc_final: 0.7913 (t)
REVERT: R  723 ILE cc_start: 0.8713 (mm) cc_final: 0.8319 (tp)
REVERT: R  791 LEU cc_start: 0.7634 (mp) cc_final: 0.7425 (mm)
REVERT: R  853 MET cc_start: 0.7331 (mtp) cc_final: 0.6914 (mtt)
REVERT: R  860 ASN cc_start: 0.7539 (m-40) cc_final: 0.7219 (m-40)
REVERT: R  868 PHE cc_start: 0.8288 (t80) cc_final: 0.8064 (t80)
REVERT: S   31 SER cc_start: 0.8599 (m) cc_final: 0.8288 (t)
REVERT: S   93 MET cc_start: 0.8104 (ttp) cc_final: 0.7848 (ttp)
REVERT: S  140 MET cc_start: 0.8829 (mmm) cc_final: 0.8348 (mmm)
REVERT: S  202 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8400 (ttm110)
REVERT: S  212 PHE cc_start: 0.8479 (m-80) cc_final: 0.8076 (m-80)
REVERT: S  230 MET cc_start: 0.8440 (tpp) cc_final: 0.8155 (tpp)
REVERT: S  231 GLN cc_start: 0.8858 (pp30) cc_final: 0.8072 (pp30)
  outliers start: 30
  outliers final: 10
  residues processed: 285
  average time/residue: 0.4640
  time to fit residues: 142.9442
Evaluate side-chains
  268 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 254
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 CYS
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  623 ILE
Chi-restraints excluded: chain R residue  838 TRP
Chi-restraints excluded: chain S residue  204 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 67 optimal weight:    0.3980
   chunk 69 optimal weight:    0.0980
   chunk 15 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 292 ASN
B  44 GLN
B 175 GLN
B 176 GLN
B 266 HIS
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
S 194 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.110786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.100032 restraints weight = 16157.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.15
r_work: 0.3302 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9621  Z= 0.133
  Angle     :  0.586   9.711  13079  Z= 0.308
  Chirality :  0.042   0.206   1496
  Planarity :  0.005   0.054   1654
  Dihedral  :  4.518  27.163   1379
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.14 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.24), residues: 1205
  helix:  0.96 (0.27), residues: 363
  sheet: -0.86 (0.27), residues: 310
  loop : -1.27 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.020   0.001   TYR R 753 
 PHE   0.014   0.002   PHE R 868 
 TRP   0.031   0.002   TRP A 281 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9617)
  covalent geometry    : angle       0.58631 (13071)
  SS BOND              : bond        0.00175 (    4)
  SS BOND              : angle       0.67592 (    8)
  hydrogen bonds       : bond        0.04104 (  434)
  hydrogen bonds       : angle       5.01386 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 289
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8115 (mmt-90)
REVERT: A   65 THR cc_start: 0.8589 (m) cc_final: 0.8202 (p)
REVERT: A  239 ASP cc_start: 0.8235 (p0) cc_final: 0.8025 (p0)
REVERT: A  260 SER cc_start: 0.8559 (m) cc_final: 0.8218 (p)
REVERT: A  265 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7827 (mtp85)
REVERT: A  268 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: A  344 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8109 (mm-30)
REVERT: A  381 ASP cc_start: 0.8501 (t0) cc_final: 0.8290 (t0)
REVERT: B   10 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7834 (tp30)
REVERT: B   17 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8465 (tt0)
REVERT: B   20 ASP cc_start: 0.8120 (m-30) cc_final: 0.7587 (m-30)
REVERT: B   29 THR cc_start: 0.8020 (t) cc_final: 0.7796 (p)
REVERT: B   65 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8064 (m)
REVERT: B  134 ARG cc_start: 0.8428 (pmm-80) cc_final: 0.7968 (ptp90)
REVERT: B  212 ASP cc_start: 0.8175 (t0) cc_final: 0.7525 (t0)
REVERT: B  217 MET cc_start: 0.8074 (ppp) cc_final: 0.7604 (ppp)
REVERT: B  228 ASP cc_start: 0.8030 (m-30) cc_final: 0.7514 (m-30)
REVERT: B  259 GLN cc_start: 0.7879 (mp10) cc_final: 0.7413 (mp10)
REVERT: B  297 TRP cc_start: 0.8780 (m100) cc_final: 0.8564 (m100)
REVERT: G   19 LEU cc_start: 0.8384 (mm) cc_final: 0.7814 (mm)
REVERT: G   21 MET cc_start: 0.8024 (tmm) cc_final: 0.7708 (ttp)
REVERT: G   62 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7396 (tmm-80)
REVERT: N    6 GLU cc_start: 0.7953 (pm20) cc_final: 0.7741 (pm20)
REVERT: N   39 GLN cc_start: 0.8636 (tt0) cc_final: 0.8430 (tt0)
REVERT: N   60 TYR cc_start: 0.8682 (m-10) cc_final: 0.8224 (m-80)
REVERT: N   67 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8041 (mtp180)
REVERT: N  113 THR cc_start: 0.8539 (m) cc_final: 0.8247 (p)
REVERT: R  691 VAL cc_start: 0.8244 (m) cc_final: 0.8011 (t)
REVERT: R  704 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8360 (mtt)
REVERT: R  791 LEU cc_start: 0.7759 (mp) cc_final: 0.7541 (mm)
REVERT: R  796 MET cc_start: 0.7883 (mpp) cc_final: 0.7680 (mmm)
REVERT: R  801 LEU cc_start: 0.8149 (mm) cc_final: 0.7922 (mt)
REVERT: R  860 ASN cc_start: 0.7486 (m-40) cc_final: 0.7199 (m-40)
REVERT: R  868 PHE cc_start: 0.8399 (t80) cc_final: 0.8178 (t80)
REVERT: S   31 SER cc_start: 0.8680 (m) cc_final: 0.8418 (p)
REVERT: S  140 MET cc_start: 0.8859 (mmm) cc_final: 0.8553 (mmm)
REVERT: S  192 MET cc_start: 0.8339 (tmm) cc_final: 0.8129 (ttm)
REVERT: S  212 PHE cc_start: 0.8611 (m-80) cc_final: 0.8101 (m-80)
REVERT: S  230 MET cc_start: 0.8368 (tpp) cc_final: 0.8129 (ttt)
REVERT: S  231 GLN cc_start: 0.8691 (pp30) cc_final: 0.8008 (pp30)
  outliers start: 37
  outliers final: 11
  residues processed: 299
  average time/residue: 0.4926
  time to fit residues: 158.1662
Evaluate side-chains
  285 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 270
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  704 MET
Chi-restraints excluded: chain R residue  838 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 292 ASN
B 175 GLN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 659 GLN
S  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.108069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.097199 restraints weight = 16266.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.13
r_work: 0.3254 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9621  Z= 0.180
  Angle     :  0.600   8.624  13079  Z= 0.315
  Chirality :  0.043   0.154   1496
  Planarity :  0.005   0.053   1654
  Dihedral  :  4.442  27.233   1377
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.67 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.24), residues: 1205
  helix:  1.16 (0.27), residues: 370
  sheet: -0.77 (0.27), residues: 310
  loop : -1.22 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG S  18 
 TYR   0.014   0.002   TYR R 753 
 PHE   0.016   0.002   PHE R 832 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 9617)
  covalent geometry    : angle       0.60023 (13071)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       0.81740 (    8)
  hydrogen bonds       : bond        0.03868 (  434)
  hydrogen bonds       : angle       4.95859 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 287
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   48 ARG cc_start: 0.8447 (mmt90) cc_final: 0.8151 (mmt-90)
REVERT: A  265 ARG cc_start: 0.8346 (mtp85) cc_final: 0.7996 (mtp85)
REVERT: A  272 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8184 (t0)
REVERT: A  296 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7969 (tt)
REVERT: A  314 GLU cc_start: 0.7123 (pm20) cc_final: 0.6916 (pm20)
REVERT: A  347 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8556 (ptp90)
REVERT: A  381 ASP cc_start: 0.8526 (t0) cc_final: 0.8319 (t0)
REVERT: B   10 GLU cc_start: 0.8421 (tp30) cc_final: 0.8080 (tp30)
REVERT: B   20 ASP cc_start: 0.8235 (m-30) cc_final: 0.7729 (m-30)
REVERT: B   29 THR cc_start: 0.8078 (t) cc_final: 0.7854 (p)
REVERT: B   43 ILE cc_start: 0.8801 (tp) cc_final: 0.8452 (pt)
REVERT: B  130 GLU cc_start: 0.7644 (tm-30) cc_final: 0.6758 (tm-30)
REVERT: B  134 ARG cc_start: 0.8542 (pmm-80) cc_final: 0.8190 (ptp90)
REVERT: B  152 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: B  212 ASP cc_start: 0.8197 (t0) cc_final: 0.7595 (t0)
REVERT: B  217 MET cc_start: 0.8108 (ppp) cc_final: 0.7886 (pp-130)
REVERT: B  228 ASP cc_start: 0.8055 (m-30) cc_final: 0.7512 (m-30)
REVERT: B  259 GLN cc_start: 0.8170 (mp10) cc_final: 0.7422 (mp10)
REVERT: B  314 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7848 (mtp85)
REVERT: G   62 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7395 (tmm-80)
REVERT: N   39 GLN cc_start: 0.8719 (tt0) cc_final: 0.8500 (tt0)
REVERT: R  623 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7782 (tt)
REVERT: R  641 THR cc_start: 0.8693 (p) cc_final: 0.8440 (t)
REVERT: R  649 ARG cc_start: 0.8823 (mtm110) cc_final: 0.8301 (mtm180)
REVERT: R  691 VAL cc_start: 0.8392 (m) cc_final: 0.8178 (t)
REVERT: R  791 LEU cc_start: 0.7986 (mp) cc_final: 0.7774 (mm)
REVERT: R  796 MET cc_start: 0.8141 (tpp) cc_final: 0.7894 (mpp)
REVERT: R  801 LEU cc_start: 0.8318 (mm) cc_final: 0.8056 (mt)
REVERT: S   69 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8556 (t)
REVERT: S  140 MET cc_start: 0.8897 (mmm) cc_final: 0.8546 (mmm)
REVERT: S  160 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7682 (ttm110)
REVERT: S  192 MET cc_start: 0.8553 (tmm) cc_final: 0.8331 (ttt)
REVERT: S  231 GLN cc_start: 0.8754 (pp30) cc_final: 0.8118 (pp30)
  outliers start: 40
  outliers final: 20
  residues processed: 302
  average time/residue: 0.5183
  time to fit residues: 167.5111
Evaluate side-chains
  292 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 265
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  623 ILE
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  640 VAL
Chi-restraints excluded: chain R residue  838 TRP
Chi-restraints excluded: chain S residue   69 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0470
   chunk 50 optimal weight:    0.2980
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 271 ASN
B 175 GLN
B 239 ASN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.108396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.097502 restraints weight = 16195.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.15
r_work: 0.3270 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9621  Z= 0.141
  Angle     :  0.587   9.491  13079  Z= 0.304
  Chirality :  0.042   0.153   1496
  Planarity :  0.005   0.051   1654
  Dihedral  :  4.374  28.784   1377
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 22.09 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.24), residues: 1205
  helix:  1.44 (0.27), residues: 363
  sheet: -0.76 (0.27), residues: 310
  loop : -1.16 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG S  18 
 TYR   0.022   0.002   TYR B 145 
 PHE   0.022   0.002   PHE R 866 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9617)
  covalent geometry    : angle       0.58725 (13071)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       0.66232 (    8)
  hydrogen bonds       : bond        0.03689 (  434)
  hydrogen bonds       : angle       4.85654 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 269
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8195 (mmt-90)
REVERT: A   65 THR cc_start: 0.8639 (m) cc_final: 0.8428 (t)
REVERT: A  272 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8151 (t0)
REVERT: A  296 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7941 (tt)
REVERT: A  314 GLU cc_start: 0.7021 (pm20) cc_final: 0.6807 (pm20)
REVERT: A  347 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8384 (ptp90)
REVERT: A  381 ASP cc_start: 0.8543 (t0) cc_final: 0.8301 (t0)
REVERT: B   10 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8044 (tp30)
REVERT: B   16 ASN cc_start: 0.8218 (m-40) cc_final: 0.7733 (m-40)
REVERT: B   20 ASP cc_start: 0.8225 (m-30) cc_final: 0.7711 (m-30)
REVERT: B   43 ILE cc_start: 0.8731 (tp) cc_final: 0.8468 (pt)
REVERT: B  130 GLU cc_start: 0.7698 (tm-30) cc_final: 0.6848 (tm-30)
REVERT: B  134 ARG cc_start: 0.8579 (pmm-80) cc_final: 0.8175 (ptp90)
REVERT: B  186 ASP cc_start: 0.7281 (t0) cc_final: 0.7040 (t0)
REVERT: B  212 ASP cc_start: 0.8152 (t0) cc_final: 0.7564 (t0)
REVERT: B  217 MET cc_start: 0.8089 (ppp) cc_final: 0.7848 (pp-130)
REVERT: B  220 GLN cc_start: 0.8352 (pt0) cc_final: 0.7918 (pt0)
REVERT: B  228 ASP cc_start: 0.8077 (m-30) cc_final: 0.7728 (m-30)
REVERT: B  259 GLN cc_start: 0.8102 (mp10) cc_final: 0.7388 (mp10)
REVERT: B  297 TRP cc_start: 0.8807 (m100) cc_final: 0.8563 (m100)
REVERT: B  314 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7765 (mtp85)
REVERT: G   50 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7647 (mt)
REVERT: G   62 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7366 (tmm-80)
REVERT: N   25 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8034 (p)
REVERT: R  623 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7761 (tt)
REVERT: R  641 THR cc_start: 0.8663 (p) cc_final: 0.8454 (t)
REVERT: R  691 VAL cc_start: 0.8390 (m) cc_final: 0.8169 (t)
REVERT: R  791 LEU cc_start: 0.8024 (mp) cc_final: 0.7816 (mm)
REVERT: R  801 LEU cc_start: 0.8340 (mm) cc_final: 0.8068 (mt)
REVERT: S  160 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7708 (ttm110)
REVERT: S  231 GLN cc_start: 0.8780 (pp30) cc_final: 0.8112 (pp30)
  outliers start: 44
  outliers final: 16
  residues processed: 283
  average time/residue: 0.5029
  time to fit residues: 152.6722
Evaluate side-chains
  284 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 260
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  623 ILE
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  827 ILE
Chi-restraints excluded: chain R residue  859 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 69 optimal weight:    0.1980
   chunk 81 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0010
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 271 ASN
A 292 ASN
B 175 GLN
B 239 ASN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 659 GLN
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.097218 restraints weight = 16214.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.16
r_work: 0.3265 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.5568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9621  Z= 0.140
  Angle     :  0.584   9.172  13079  Z= 0.303
  Chirality :  0.042   0.173   1496
  Planarity :  0.005   0.051   1654
  Dihedral  :  4.309  30.328   1377
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 24.72 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.24), residues: 1205
  helix:  1.41 (0.26), residues: 370
  sheet: -0.67 (0.27), residues: 309
  loop : -1.08 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 283 
 TYR   0.020   0.002   TYR N  60 
 PHE   0.027   0.002   PHE R 868 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9617)
  covalent geometry    : angle       0.58376 (13071)
  SS BOND              : bond        0.00232 (    4)
  SS BOND              : angle       0.59306 (    8)
  hydrogen bonds       : bond        0.03610 (  434)
  hydrogen bonds       : angle       4.79395 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 268
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8885 (tttp) cc_final: 0.8617 (tttm)
REVERT: A   48 ARG cc_start: 0.8476 (mmt90) cc_final: 0.8223 (mmt-90)
REVERT: A  272 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8117 (t0)
REVERT: A  296 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8034 (tt)
REVERT: A  314 GLU cc_start: 0.6985 (pm20) cc_final: 0.6740 (pm20)
REVERT: A  347 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8403 (ptp90)
REVERT: A  381 ASP cc_start: 0.8558 (t0) cc_final: 0.8295 (t0)
REVERT: A  392 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7537 (mm-30)
REVERT: B   10 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8095 (tp30)
REVERT: B   16 ASN cc_start: 0.8239 (m-40) cc_final: 0.7601 (t0)
REVERT: B   20 ASP cc_start: 0.8225 (m-30) cc_final: 0.7729 (m-30)
REVERT: B   43 ILE cc_start: 0.8640 (tp) cc_final: 0.8423 (pt)
REVERT: B  130 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7009 (tm-30)
REVERT: B  134 ARG cc_start: 0.8596 (pmm-80) cc_final: 0.8269 (ptp90)
REVERT: B  161 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8379 (p)
REVERT: B  186 ASP cc_start: 0.7483 (t0) cc_final: 0.7239 (t0)
REVERT: B  212 ASP cc_start: 0.8126 (t0) cc_final: 0.7643 (t0)
REVERT: B  217 MET cc_start: 0.8060 (ppp) cc_final: 0.7855 (pp-130)
REVERT: B  220 GLN cc_start: 0.8380 (pt0) cc_final: 0.8057 (pt0)
REVERT: B  228 ASP cc_start: 0.8103 (m-30) cc_final: 0.7729 (m-30)
REVERT: B  259 GLN cc_start: 0.7999 (mp10) cc_final: 0.7299 (mp10)
REVERT: B  314 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7848 (mtp180)
REVERT: G   21 MET cc_start: 0.8143 (tmm) cc_final: 0.7664 (mtp)
REVERT: G   22 GLU cc_start: 0.8025 (tp30) cc_final: 0.7486 (tp30)
REVERT: G   62 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7324 (tmm-80)
REVERT: N   25 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.8121 (p)
REVERT: R  623 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7728 (tp)
REVERT: R  649 ARG cc_start: 0.8845 (mtm110) cc_final: 0.8578 (mtm110)
REVERT: R  691 VAL cc_start: 0.8386 (m) cc_final: 0.8182 (t)
REVERT: R  791 LEU cc_start: 0.8035 (mp) cc_final: 0.7834 (mm)
REVERT: R  796 MET cc_start: 0.8038 (mmm) cc_final: 0.7810 (mpp)
REVERT: R  801 LEU cc_start: 0.8303 (mm) cc_final: 0.8046 (mt)
REVERT: R  871 TYR cc_start: 0.7859 (m-80) cc_final: 0.7530 (m-80)
REVERT: S   90 ASP cc_start: 0.8558 (m-30) cc_final: 0.8346 (m-30)
REVERT: S  160 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7664 (ttm110)
REVERT: S  178 LEU cc_start: 0.8805 (tm) cc_final: 0.8547 (tt)
REVERT: S  194 ASN cc_start: 0.8792 (m-40) cc_final: 0.8547 (m-40)
REVERT: S  231 GLN cc_start: 0.8904 (pp30) cc_final: 0.8178 (pp30)
  outliers start: 33
  outliers final: 15
  residues processed: 287
  average time/residue: 0.4823
  time to fit residues: 148.6210
Evaluate side-chains
  279 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 256
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  623 ILE
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  827 ILE
Chi-restraints excluded: chain R residue  859 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0040
   chunk 63 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0970
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 271 ASN
A 292 ASN
B  75 GLN
B 156 GLN
B 175 GLN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.109157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.098389 restraints weight = 16220.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.14
r_work: 0.3289 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9621  Z= 0.135
  Angle     :  0.587   9.316  13079  Z= 0.305
  Chirality :  0.042   0.174   1496
  Planarity :  0.005   0.051   1654
  Dihedral  :  4.294  31.019   1377
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 25.13 %
    Favored  : 70.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.24), residues: 1205
  helix:  1.55 (0.26), residues: 364
  sheet: -0.70 (0.27), residues: 313
  loop : -1.06 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 129 
 TYR   0.016   0.002   TYR B 145 
 PHE   0.024   0.002   PHE R 868 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9617)
  covalent geometry    : angle       0.58699 (13071)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       0.53281 (    8)
  hydrogen bonds       : bond        0.03614 (  434)
  hydrogen bonds       : angle       4.73109 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 267
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 SER cc_start: 0.8202 (t) cc_final: 0.7495 (p)
REVERT: A   48 ARG cc_start: 0.8480 (mmt90) cc_final: 0.8234 (mmt-90)
REVERT: A  272 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8118 (t0)
REVERT: A  296 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8052 (tt)
REVERT: A  314 GLU cc_start: 0.6982 (pm20) cc_final: 0.6728 (pm20)
REVERT: A  347 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8218 (ptp90)
REVERT: A  381 ASP cc_start: 0.8555 (t0) cc_final: 0.8309 (t0)
REVERT: A  392 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7508 (mm-30)
REVERT: B   10 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7963 (tp30)
REVERT: B   16 ASN cc_start: 0.8279 (m-40) cc_final: 0.7625 (t0)
REVERT: B   20 ASP cc_start: 0.8206 (m-30) cc_final: 0.7756 (m-30)
REVERT: B  130 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7030 (tm-30)
REVERT: B  134 ARG cc_start: 0.8585 (pmm-80) cc_final: 0.8230 (ptp90)
REVERT: B  212 ASP cc_start: 0.8066 (t0) cc_final: 0.7667 (t0)
REVERT: B  220 GLN cc_start: 0.8317 (pt0) cc_final: 0.7931 (pt0)
REVERT: B  228 ASP cc_start: 0.8046 (m-30) cc_final: 0.7680 (m-30)
REVERT: B  259 GLN cc_start: 0.7973 (mp10) cc_final: 0.7317 (mp10)
REVERT: B  295 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8360 (t0)
REVERT: B  314 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7869 (mtp85)
REVERT: G   21 MET cc_start: 0.8180 (tmm) cc_final: 0.7874 (ttp)
REVERT: G   22 GLU cc_start: 0.7944 (tp30) cc_final: 0.7446 (tp30)
REVERT: G   62 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7247 (tmm-80)
REVERT: N   25 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8137 (p)
REVERT: N  113 THR cc_start: 0.8632 (m) cc_final: 0.8353 (p)
REVERT: R  623 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7614 (tp)
REVERT: R  691 VAL cc_start: 0.8418 (m) cc_final: 0.8208 (t)
REVERT: R  801 LEU cc_start: 0.8382 (mm) cc_final: 0.8117 (mt)
REVERT: S   90 ASP cc_start: 0.8567 (m-30) cc_final: 0.8305 (m-30)
REVERT: S  141 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8572 (p)
REVERT: S  160 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7653 (ttm110)
REVERT: S  178 LEU cc_start: 0.8817 (tm) cc_final: 0.8560 (tt)
REVERT: S  194 ASN cc_start: 0.8845 (m-40) cc_final: 0.8571 (m-40)
REVERT: S  231 GLN cc_start: 0.8897 (pp30) cc_final: 0.8214 (pp30)
  outliers start: 39
  outliers final: 17
  residues processed: 294
  average time/residue: 0.5300
  time to fit residues: 166.3399
Evaluate side-chains
  277 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 251
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  623 ILE
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  827 ILE
Chi-restraints excluded: chain R residue  859 PHE
Chi-restraints excluded: chain S residue  141 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 88 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 102 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 246 GLN
A 271 ASN
A 292 ASN
B 175 GLN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 659 GLN
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.097249 restraints weight = 16128.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.12
r_work: 0.3260 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.5898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9621  Z= 0.168
  Angle     :  0.612   9.392  13079  Z= 0.318
  Chirality :  0.043   0.180   1496
  Planarity :  0.005   0.052   1654
  Dihedral  :  4.341  26.711   1377
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 26.24 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.24), residues: 1205
  helix:  1.47 (0.26), residues: 370
  sheet: -0.62 (0.27), residues: 311
  loop : -1.04 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N  67 
 TYR   0.027   0.002   TYR B 145 
 PHE   0.016   0.001   PHE R 832 
 TRP   0.014   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9617)
  covalent geometry    : angle       0.61240 (13071)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       0.62668 (    8)
  hydrogen bonds       : bond        0.03664 (  434)
  hydrogen bonds       : angle       4.75704 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 261
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 SER cc_start: 0.8247 (t) cc_final: 0.7571 (p)
REVERT: A   35 MET cc_start: 0.8462 (mpp) cc_final: 0.8099 (mmm)
REVERT: A   44 LYS cc_start: 0.8901 (tttt) cc_final: 0.8650 (tttm)
REVERT: A  263 TYR cc_start: 0.8565 (m-80) cc_final: 0.8360 (m-80)
REVERT: A  272 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8107 (t0)
REVERT: A  347 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8265 (ptp90)
REVERT: A  381 ASP cc_start: 0.8571 (t0) cc_final: 0.8305 (t0)
REVERT: A  392 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7512 (mm-30)
REVERT: B   10 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7992 (tp30)
REVERT: B   16 ASN cc_start: 0.8292 (m-40) cc_final: 0.7681 (t0)
REVERT: B   20 ASP cc_start: 0.8249 (m-30) cc_final: 0.7830 (m-30)
REVERT: B  130 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7014 (tm-30)
REVERT: B  134 ARG cc_start: 0.8594 (pmm-80) cc_final: 0.8221 (ptp90)
REVERT: B  212 ASP cc_start: 0.8076 (t0) cc_final: 0.7667 (t0)
REVERT: B  220 GLN cc_start: 0.8348 (pt0) cc_final: 0.7897 (pt0)
REVERT: B  228 ASP cc_start: 0.8074 (m-30) cc_final: 0.7682 (m-30)
REVERT: B  259 GLN cc_start: 0.8146 (mp10) cc_final: 0.7550 (mp10)
REVERT: B  297 TRP cc_start: 0.8808 (m100) cc_final: 0.8556 (m100)
REVERT: B  316 SER cc_start: 0.8452 (t) cc_final: 0.8250 (t)
REVERT: G   22 GLU cc_start: 0.7993 (tp30) cc_final: 0.7541 (tp30)
REVERT: G   62 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7282 (tmm-80)
REVERT: N   25 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8100 (p)
REVERT: N   67 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (mtm180)
REVERT: N   87 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7839 (mtmm)
REVERT: N  113 THR cc_start: 0.8678 (m) cc_final: 0.8415 (p)
REVERT: R  623 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7629 (tp)
REVERT: R  801 LEU cc_start: 0.8424 (mm) cc_final: 0.8165 (mt)
REVERT: S   90 ASP cc_start: 0.8569 (m-30) cc_final: 0.8349 (m-30)
REVERT: S  160 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7611 (ttm110)
REVERT: S  220 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7523 (mt-10)
REVERT: S  231 GLN cc_start: 0.8850 (pp30) cc_final: 0.8195 (pp30)
  outliers start: 34
  outliers final: 20
  residues processed: 281
  average time/residue: 0.5394
  time to fit residues: 161.9890
Evaluate side-chains
  274 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 247
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue  623 ILE
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  827 ILE
Chi-restraints excluded: chain R residue  859 PHE
Chi-restraints excluded: chain S residue  141 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 29 optimal weight:    0.0060
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 115 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0980
   chunk 118 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0010
   overall best weight:    0.2402

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 246 GLN
A 292 ASN
B 175 GLN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.110411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.099703 restraints weight = 16150.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.14
r_work: 0.3310 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.5977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9621  Z= 0.123
  Angle     :  0.606   9.673  13079  Z= 0.313
  Chirality :  0.042   0.169   1496
  Planarity :  0.005   0.051   1654
  Dihedral  :  4.285  28.807   1377
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 27.96 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.24), residues: 1205
  helix:  1.65 (0.27), residues: 364
  sheet: -0.64 (0.27), residues: 314
  loop : -1.04 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 304 
 TYR   0.024   0.002   TYR B 145 
 PHE   0.014   0.001   PHE R 843 
 TRP   0.015   0.001   TRP A 244 
 HIS   0.005   0.001   HIS A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9617)
  covalent geometry    : angle       0.60572 (13071)
  SS BOND              : bond        0.00277 (    4)
  SS BOND              : angle       0.49955 (    8)
  hydrogen bonds       : bond        0.03540 (  434)
  hydrogen bonds       : angle       4.66969 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 262
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 SER cc_start: 0.8193 (t) cc_final: 0.7476 (p)
REVERT: A   35 MET cc_start: 0.8387 (mpp) cc_final: 0.8144 (mmm)
REVERT: A   44 LYS cc_start: 0.8894 (tttt) cc_final: 0.8659 (tttm)
REVERT: A  272 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8109 (t0)
REVERT: A  347 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8242 (ptp90)
REVERT: A  381 ASP cc_start: 0.8554 (t0) cc_final: 0.8294 (t0)
REVERT: A  392 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7450 (mm-30)
REVERT: B   10 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7792 (tp30)
REVERT: B   16 ASN cc_start: 0.8266 (m-40) cc_final: 0.7596 (t0)
REVERT: B   20 ASP cc_start: 0.8201 (m-30) cc_final: 0.7748 (m-30)
REVERT: B  130 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7086 (tm-30)
REVERT: B  134 ARG cc_start: 0.8550 (pmm-80) cc_final: 0.8285 (ptp90)
REVERT: B  137 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7947 (ttm-80)
REVERT: B  186 ASP cc_start: 0.7425 (t0) cc_final: 0.7160 (t0)
REVERT: B  212 ASP cc_start: 0.7953 (t0) cc_final: 0.7557 (t0)
REVERT: B  220 GLN cc_start: 0.8302 (pt0) cc_final: 0.7907 (pt0)
REVERT: B  228 ASP cc_start: 0.8069 (m-30) cc_final: 0.7662 (m-30)
REVERT: B  239 ASN cc_start: 0.8624 (m-40) cc_final: 0.8395 (m-40)
REVERT: B  253 PHE cc_start: 0.8314 (m-80) cc_final: 0.8082 (m-80)
REVERT: B  259 GLN cc_start: 0.7975 (mp10) cc_final: 0.7340 (mp10)
REVERT: B  314 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7843 (mtp180)
REVERT: G   19 LEU cc_start: 0.8658 (mm) cc_final: 0.8196 (mm)
REVERT: G   22 GLU cc_start: 0.7924 (tp30) cc_final: 0.7496 (tp30)
REVERT: G   62 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7264 (tmm-80)
REVERT: N   34 MET cc_start: 0.8805 (mmm) cc_final: 0.7935 (mmm)
REVERT: N   67 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8204 (mtm180)
REVERT: N   87 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7827 (mtmm)
REVERT: N  113 THR cc_start: 0.8689 (m) cc_final: 0.8441 (p)
REVERT: R  801 LEU cc_start: 0.8405 (mm) cc_final: 0.8139 (mt)
REVERT: S   18 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7974 (ttm-80)
REVERT: S   90 ASP cc_start: 0.8521 (m-30) cc_final: 0.8224 (m-30)
REVERT: S  160 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7562 (ttm110)
REVERT: S  178 LEU cc_start: 0.8867 (tm) cc_final: 0.8637 (tt)
REVERT: S  194 ASN cc_start: 0.8833 (m-40) cc_final: 0.8558 (m-40)
REVERT: S  220 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7515 (mt-10)
REVERT: S  231 GLN cc_start: 0.8852 (pp30) cc_final: 0.8210 (pp30)
  outliers start: 28
  outliers final: 19
  residues processed: 280
  average time/residue: 0.5149
  time to fit residues: 153.7066
Evaluate side-chains
  280 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 257
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  827 ILE
Chi-restraints excluded: chain R residue  859 PHE
Chi-restraints excluded: chain S residue  141 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0020
   chunk 104 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 117 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 85 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 292 ASN
B 156 GLN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 659 GLN
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.108881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.098092 restraints weight = 16213.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.15
r_work: 0.3279 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.6057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9621  Z= 0.153
  Angle     :  0.624   9.606  13079  Z= 0.323
  Chirality :  0.043   0.164   1496
  Planarity :  0.005   0.052   1654
  Dihedral  :  4.331  28.694   1377
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 28.37 %
    Favored  : 69.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.24), residues: 1205
  helix:  1.64 (0.27), residues: 364
  sheet: -0.64 (0.27), residues: 314
  loop : -1.00 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 283 
 TYR   0.022   0.002   TYR R 712 
 PHE   0.017   0.001   PHE R 843 
 TRP   0.016   0.001   TRP A 244 
 HIS   0.005   0.001   HIS A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9617)
  covalent geometry    : angle       0.62420 (13071)
  SS BOND              : bond        0.00288 (    4)
  SS BOND              : angle       0.51326 (    8)
  hydrogen bonds       : bond        0.03600 (  434)
  hydrogen bonds       : angle       4.67363 ( 1230)

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

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

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2410 Ramachandran restraints generated.
    1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 258
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 SER cc_start: 0.8236 (t) cc_final: 0.7544 (p)
REVERT: A   35 MET cc_start: 0.8492 (mpp) cc_final: 0.8130 (mmm)
REVERT: A   44 LYS cc_start: 0.8921 (tttt) cc_final: 0.8674 (tttm)
REVERT: A  263 TYR cc_start: 0.8559 (m-80) cc_final: 0.8318 (m-80)
REVERT: A  272 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8134 (t0)
REVERT: A  347 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8240 (ptp90)
REVERT: A  381 ASP cc_start: 0.8571 (t0) cc_final: 0.8311 (t0)
REVERT: A  389 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8223 (ttm-80)
REVERT: A  392 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7479 (mm-30)
REVERT: B   10 GLU cc_start: 0.8278 (tp30) cc_final: 0.7847 (tp30)
REVERT: B   96 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7405 (mtt90)
REVERT: B  130 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7109 (tm-30)
REVERT: B  134 ARG cc_start: 0.8578 (pmm-80) cc_final: 0.8310 (ptp90)
REVERT: B  186 ASP cc_start: 0.7617 (t0) cc_final: 0.7381 (t0)
REVERT: B  212 ASP cc_start: 0.8000 (t0) cc_final: 0.7574 (t0)
REVERT: B  220 GLN cc_start: 0.8324 (pt0) cc_final: 0.7896 (pt0)
REVERT: B  228 ASP cc_start: 0.8148 (m-30) cc_final: 0.7808 (m-30)
REVERT: B  239 ASN cc_start: 0.8599 (m-40) cc_final: 0.8365 (m-40)
REVERT: B  253 PHE cc_start: 0.8310 (m-80) cc_final: 0.8066 (m-80)
REVERT: B  259 GLN cc_start: 0.8104 (mp10) cc_final: 0.7469 (mp10)
REVERT: B  314 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7863 (mtp180)
REVERT: G   19 LEU cc_start: 0.8674 (mm) cc_final: 0.8214 (mm)
REVERT: G   22 GLU cc_start: 0.7936 (tp30) cc_final: 0.7510 (tp30)
REVERT: G   62 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7281 (tmm-80)
REVERT: N  113 THR cc_start: 0.8641 (m) cc_final: 0.8415 (p)
REVERT: R  801 LEU cc_start: 0.8426 (mm) cc_final: 0.8169 (mt)
REVERT: S   18 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7954 (ttm-80)
REVERT: S   38 ARG cc_start: 0.8939 (ptt-90) cc_final: 0.8708 (ptt-90)
REVERT: S   76 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8184 (mtmt)
REVERT: S  160 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7622 (ttm110)
REVERT: S  194 ASN cc_start: 0.8863 (m-40) cc_final: 0.8597 (m110)
REVERT: S  220 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7455 (mt-10)
REVERT: S  231 GLN cc_start: 0.8908 (pp30) cc_final: 0.8269 (pp30)
  outliers start: 26
  outliers final: 18
  residues processed: 275
  average time/residue: 0.4750
  time to fit residues: 139.4547
Evaluate side-chains
  276 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 255
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  624 THR
Chi-restraints excluded: chain R residue  827 ILE
Chi-restraints excluded: chain R residue  853 MET
Chi-restraints excluded: chain R residue  859 PHE
Chi-restraints excluded: chain S residue  141 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 292 ASN
B  32 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 175 GLN
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
** R 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.096419 restraints weight = 16003.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.15
r_work: 0.3255 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.6157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9621  Z= 0.184
  Angle     :  0.648   9.530  13079  Z= 0.335
  Chirality :  0.044   0.158   1496
  Planarity :  0.005   0.052   1654
  Dihedral  :  4.452  27.799   1377
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 28.77 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.24), residues: 1205
  helix:  1.53 (0.26), residues: 370
  sheet: -0.55 (0.28), residues: 311
  loop : -0.96 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 283 
 TYR   0.022   0.002   TYR N  60 
 PHE   0.023   0.002   PHE R 866 
 TRP   0.016   0.001   TRP A 244 
 HIS   0.005   0.001   HIS A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9617)
  covalent geometry    : angle       0.64810 (13071)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       0.71393 (    8)
  hydrogen bonds       : bond        0.03739 (  434)
  hydrogen bonds       : angle       4.72495 ( 1230)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3726.00 seconds
wall clock time: 64 minutes 12.27 seconds (3852.27 seconds total)