Starting phenix.real_space_refine
on Sat Aug  3 13:25:16 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/08_2024/8wst_37824.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/08_2024/8wst_37824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/08_2024/8wst_37824.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/08_2024/8wst_37824.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/08_2024/8wst_37824.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/08_2024/8wst_37824.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5261      2.51       5
     N    1432      2.21       5
     O    1534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   40": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 8286
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1876
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2590
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen planarities: 1
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "L"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 129
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 13}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 973
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 2280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2280
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 14, 'TRANS': 272}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 5.14, per 1000 atoms: 0.62
  Number of scatterers: 8286
  At special positions: 0
  Unit cell: (83.22, 100.01, 133.59, 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      59     16.00
     O    1534      8.00
     N    1432      7.00
     C    5261      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, 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=2.03
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 184 " distance=1.99

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 3.16
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1986

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      40.9% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.590A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 4.135A  pdb=" N   ARG A 135 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.118A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 203
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 5 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 3.505A  pdb=" N   ARG G  13 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.623A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 32 through 62
      removed outlier: 3.980A  pdb=" N   LEU R  37 " --> pdb=" O   ASP R  33 " (cutoff:3.500A)
      Proline residue:  R  38  - end of helix
      removed outlier: 4.224A  pdb=" N   ILE R  41 " --> pdb=" O   LEU R  37 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY R  42 " --> pdb=" O   PRO R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 85
    Processing helix  chain 'R' and resid 85 through 96
      removed outlier: 3.671A  pdb=" N   LEU R  89 " --> pdb=" O   GLY R  85 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLN R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   TRP R  93 " --> pdb=" O   LEU R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 142 through 145
    Processing helix  chain 'R' and resid 146 through 165
      removed outlier: 3.593A  pdb=" N   ALA R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.552A  pdb=" N   TRP R 169 " --> pdb=" O   ALA R 165 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL R 170 " --> pdb=" O   LEU R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 181
      removed outlier: 4.328A  pdb=" N   VAL R 181 " --> pdb=" O   LYS R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 206
    Processing helix  chain 'R' and resid 208 through 231
      removed outlier: 3.809A  pdb=" N   LEU R 212 " --> pdb=" O   PHE R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 235
    Processing helix  chain 'R' and resid 247 through 249
      No H-bonds generated for 'chain 'R' and resid 247 through 249'
    Processing helix  chain 'R' and resid 250 through 276
      Proline residue:  R 266  - end of helix
      removed outlier: 3.561A  pdb=" N   LEU R 272 " --> pdb=" O   HIS R 268 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLN R 276 " --> pdb=" O   LEU R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 296
      removed outlier: 4.047A  pdb=" N   TYR R 296 " --> pdb=" O   ILE R 292 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 296 through 308
      removed outlier: 3.620A  pdb=" N   SER R 300 " --> pdb=" O   TYR R 296 " (cutoff:3.500A)
      Proline residue:  R 303  - end of helix
    Processing helix  chain 'R' and resid 313 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76
      removed outlier: 6.260A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 9.347A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 9.056A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.999A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.759A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.969A  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: 6.908A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.797A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.601A  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: 3.631A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.432A  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: 3.951A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.571A  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 278
      removed outlier: 3.895A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 7 through 9
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.588A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.162A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 172 through 175

    408 hydrogen bonds defined for protein.
    1137 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 3.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2705
        1.35 -     1.46: 1989
        1.46 -     1.58: 3681
        1.58 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 8457
  Sorted by residual:
  bond pdb=" N   GLU R 182 "
       pdb=" CA  GLU R 182 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.29e-02 6.01e+03 8.19e+00
  bond pdb=" N   VAL A  86 "
       pdb=" CA  VAL A  86 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.07e+00
  bond pdb=" N   GLN A  89 "
       pdb=" CA  GLN A  89 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.033 1.29e-02 6.01e+03 6.50e+00
  bond pdb=" N   SER R 183 "
       pdb=" CA  SER R 183 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.27e-02 6.20e+03 6.27e+00
  bond pdb=" N   VAL R 181 "
       pdb=" CA  VAL R 181 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.25e-02 6.40e+03 5.75e+00
  ... (remaining 8452 not shown)

  Histogram of bond angle deviations from ideal:
      100.46 -   107.17: 216
      107.17 -   113.87: 4738
      113.87 -   120.58: 3382
      120.58 -   127.29: 3044
      127.29 -   133.99: 91
  Bond angle restraints: 11471
  Sorted by residual:
  angle pdb=" C   CYS R 184 "
        pdb=" CA  CYS R 184 "
        pdb=" CB  CYS R 184 "
      ideal   model   delta    sigma   weight residual
     110.88  105.02    5.86 1.60e+00 3.91e-01 1.34e+01
  angle pdb=" N   ASP A  85 "
        pdb=" CA  ASP A  85 "
        pdb=" C   ASP A  85 "
      ideal   model   delta    sigma   weight residual
     107.99  101.56    6.43 1.77e+00 3.19e-01 1.32e+01
  angle pdb=" N   CYS R 184 "
        pdb=" CA  CYS R 184 "
        pdb=" C   CYS R 184 "
      ideal   model   delta    sigma   weight residual
     108.63  103.01    5.62 1.60e+00 3.91e-01 1.23e+01
  angle pdb=" N   SER R 183 "
        pdb=" CA  SER R 183 "
        pdb=" C   SER R 183 "
      ideal   model   delta    sigma   weight residual
     109.07  114.41   -5.34 1.52e+00 4.33e-01 1.23e+01
  angle pdb=" C   GLU R 182 "
        pdb=" N   SER R 183 "
        pdb=" CA  SER R 183 "
      ideal   model   delta    sigma   weight residual
     121.75  116.01    5.74 1.73e+00 3.34e-01 1.10e+01
  ... (remaining 11466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 4890
       17.50 -    35.00: 125
       35.00 -    52.49: 28
       52.49 -    69.99: 5
       69.99 -    87.49: 4
  Dihedral angle restraints: 5052
    sinusoidal: 1979
      harmonic: 3073
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.36  -60.36     1      1.00e+01 1.00e-02 4.85e+01
  dihedral pdb=" C   CYS R 184 "
           pdb=" N   CYS R 184 "
           pdb=" CA  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.35  -11.25     0      2.50e+00 1.60e-01 2.02e+01
  dihedral pdb=" N   CYS R 184 "
           pdb=" C   CYS R 184 "
           pdb=" CA  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.64    8.16     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 5049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1220
       0.082 -    0.163: 81
       0.163 -    0.245: 2
       0.245 -    0.327: 0
       0.327 -    0.408: 1
  Chirality restraints: 1304
  Sorted by residual:
  chirality pdb=" CA  CYS R 184 "
            pdb=" N   CYS R 184 "
            pdb=" C   CYS R 184 "
            pdb=" CB  CYS R 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.92   -0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" CA  VAL R 181 "
            pdb=" N   VAL R 181 "
            pdb=" C   VAL R 181 "
            pdb=" CB  VAL R 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  VAL A  86 "
            pdb=" N   VAL A  86 "
            pdb=" C   VAL A  86 "
            pdb=" CB  VAL A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.18 2.00e-01 2.50e+01 8.46e-01
  ... (remaining 1301 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 184 "   -0.007 2.00e-02 2.50e+03   1.33e-02 1.76e+00
        pdb=" C   CYS R 184 "    0.023 2.00e-02 2.50e+03
        pdb=" O   CYS R 184 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ALA R 185 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 180 "   -0.006 2.00e-02 2.50e+03   1.22e-02 1.48e+00
        pdb=" C   GLY R 180 "    0.021 2.00e-02 2.50e+03
        pdb=" O   GLY R 180 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   VAL R 181 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 203 "    0.006 2.00e-02 2.50e+03   1.10e-02 1.22e+00
        pdb=" C   ILE R 203 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE R 203 "    0.007 2.00e-02 2.50e+03
        pdb=" N   THR R 204 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 225
        2.71 -     3.25: 8403
        3.25 -     3.80: 13293
        3.80 -     4.35: 17161
        4.35 -     4.90: 29572
  Nonbonded interactions: 68654
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OH  TYR N  32 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   LEU R 164 "
            pdb=" OH  TYR R 200 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   PHE N  29 "
            pdb=" NH2 ARG N  72 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" NH1 ARG B 283 "
            pdb=" OD1 ASP B 298 "
     model   vdw
     2.269 3.120
  ... (remaining 68649 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:                  0.010
  Normalize map: mean=0, sd=1:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     26.430
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   42.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
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      :  0.002   0.037   8457  Z= 0.140
  Angle     :  0.449   6.429  11471  Z= 0.260
  Chirality :  0.041   0.408   1304
  Planarity :  0.002   0.028   1460
  Dihedral  :  8.866  87.491   3057
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.77 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.28), residues: 1041
  helix:  3.55 (0.27), residues: 383
  sheet:  1.45 (0.36), residues: 217
  loop : -0.12 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  96 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.006   0.001   PHE A 228 
 TYR   0.008   0.001   TYR R 148 
 ARG   0.002   0.000   ARG B 214 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 196
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7306 (ttmm)
REVERT: A  221 THR cc_start: 0.7341 (p) cc_final: 0.7068 (p)
REVERT: B  325 MET cc_start: 0.8336 (mmt) cc_final: 0.8102 (mmt)
REVERT: N    5 GLN cc_start: 0.5573 (mm-40) cc_final: 0.5205 (mm110)
REVERT: N   49 SER cc_start: 0.7623 (p) cc_final: 0.7056 (t)
REVERT: R   98 GLU cc_start: 0.6329 (tt0) cc_final: 0.6076 (tt0)
REVERT: R  140 ARG cc_start: 0.5925 (tpp80) cc_final: 0.5404 (tpt90)
REVERT: R  247 MET cc_start: 0.5781 (mmm) cc_final: 0.5440 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 198
  average time/residue: 1.2652
  time to fit residues: 264.7319
Evaluate side-chains
  112 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0370
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0170
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
B  75 GLN
B 220 GLN
B 237 ASN
B 268 ASN
B 340 ASN
R 230 GLN
R 268 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8457  Z= 0.165
  Angle     :  0.530   7.218  11471  Z= 0.275
  Chirality :  0.042   0.143   1304
  Planarity :  0.004   0.044   1460
  Dihedral  :  3.785  18.752   1152
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.86 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.27), residues: 1041
  helix:  3.12 (0.27), residues: 387
  sheet:  1.28 (0.34), residues: 226
  loop : -0.25 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.012   0.001   TYR R 148 
 ARG   0.007   0.001   ARG B 137 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5737 (mt-10)
REVERT: A  221 THR cc_start: 0.7324 (p) cc_final: 0.7064 (p)
REVERT: B   59 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7300 (m-80)
REVERT: N   49 SER cc_start: 0.7698 (p) cc_final: 0.7234 (t)
REVERT: R   98 GLU cc_start: 0.6229 (tt0) cc_final: 0.5974 (tt0)
REVERT: R  140 ARG cc_start: 0.5875 (tpp80) cc_final: 0.5362 (tpt90)
REVERT: R  247 MET cc_start: 0.5818 (mmm) cc_final: 0.5484 (mmt)
  outliers start: 28
  outliers final: 8
  residues processed: 136
  average time/residue: 1.1336
  time to fit residues: 164.9782
Evaluate side-chains
  115 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  263 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0030
   chunk 63 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 74 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.8394

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 237 ASN
B 268 ASN
R 230 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8457  Z= 0.198
  Angle     :  0.555   9.881  11471  Z= 0.288
  Chirality :  0.043   0.136   1304
  Planarity :  0.004   0.037   1460
  Dihedral  :  4.176  19.569   1152
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 10.64 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.27), residues: 1041
  helix:  2.74 (0.26), residues: 393
  sheet:  1.02 (0.32), residues: 231
  loop : -0.43 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.012   0.001   TYR A 191 
 ARG   0.006   0.001   ARG B 314 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 1.058 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5651 (mt-10)
REVERT: A  221 THR cc_start: 0.7355 (p) cc_final: 0.7083 (p)
REVERT: B   59 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7468 (m-80)
REVERT: B  262 MET cc_start: 0.7449 (ttm) cc_final: 0.7224 (ttp)
REVERT: R   54 LEU cc_start: 0.7558 (tt) cc_final: 0.7349 (tp)
REVERT: R   98 GLU cc_start: 0.6279 (tt0) cc_final: 0.6016 (tt0)
REVERT: R  140 ARG cc_start: 0.5930 (tpp80) cc_final: 0.5422 (tpt90)
REVERT: R  232 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5808 (mmtm)
REVERT: R  247 MET cc_start: 0.5901 (mmm) cc_final: 0.5583 (mmt)
REVERT: R  252 MET cc_start: 0.7330 (ttp) cc_final: 0.7124 (ttm)
  outliers start: 33
  outliers final: 14
  residues processed: 133
  average time/residue: 1.2912
  time to fit residues: 181.8612
Evaluate side-chains
  112 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.3980
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
R  52 ASN
R 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8457  Z= 0.250
  Angle     :  0.578   7.586  11471  Z= 0.306
  Chirality :  0.044   0.143   1304
  Planarity :  0.004   0.040   1460
  Dihedral  :  4.564  20.364   1152
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 11.97 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1041
  helix:  2.38 (0.26), residues: 395
  sheet:  0.80 (0.32), residues: 220
  loop : -0.73 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.002   HIS A 209 
 PHE   0.016   0.002   PHE B 199 
 TYR   0.018   0.002   TYR A 191 
 ARG   0.004   0.001   ARG A 188 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5602 (mt-10)
REVERT: B  304 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7444 (mtm180)
REVERT: R   54 LEU cc_start: 0.7659 (tt) cc_final: 0.7431 (tp)
REVERT: R  140 ARG cc_start: 0.6021 (tpp80) cc_final: 0.5490 (tpt90)
REVERT: R  232 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5911 (mmtm)
REVERT: R  252 MET cc_start: 0.7347 (ttp) cc_final: 0.7141 (ttm)
REVERT: R  282 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6420 (tp)
  outliers start: 33
  outliers final: 15
  residues processed: 133
  average time/residue: 1.1856
  time to fit residues: 167.7791
Evaluate side-chains
  120 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0970
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8457  Z= 0.214
  Angle     :  0.548  10.003  11471  Z= 0.287
  Chirality :  0.043   0.142   1304
  Planarity :  0.004   0.049   1460
  Dihedral  :  4.467  20.408   1152
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 13.08 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.26), residues: 1041
  helix:  2.41 (0.25), residues: 394
  sheet:  0.74 (0.32), residues: 218
  loop : -0.87 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.016   0.001   TYR A 191 
 ARG   0.006   0.000   ARG A 132 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7634 (ttmm)
REVERT: A   28 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5649 (mt-10)
REVERT: B  217 MET cc_start: 0.8108 (pmt) cc_final: 0.7888 (ppp)
REVERT: G   47 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7431 (pt0)
REVERT: R   54 LEU cc_start: 0.7709 (tt) cc_final: 0.7495 (tp)
REVERT: R  140 ARG cc_start: 0.5953 (tpp80) cc_final: 0.5465 (tpt90)
REVERT: R  195 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6594 (tm)
REVERT: R  232 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5922 (mmtm)
REVERT: R  252 MET cc_start: 0.7336 (ttp) cc_final: 0.7119 (ttm)
REVERT: R  282 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6417 (OUTLIER)
  outliers start: 35
  outliers final: 19
  residues processed: 131
  average time/residue: 1.2377
  time to fit residues: 172.3007
Evaluate side-chains
  128 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    0.2980
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 95 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 237 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8457  Z= 0.153
  Angle     :  0.497   8.641  11471  Z= 0.260
  Chirality :  0.041   0.138   1304
  Planarity :  0.004   0.040   1460
  Dihedral  :  4.214  19.361   1152
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 14.08 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1041
  helix:  2.69 (0.25), residues: 393
  sheet:  0.79 (0.32), residues: 218
  loop : -0.79 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.011   0.001   TYR A 191 
 ARG   0.008   0.000   ARG A 132 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5583 (mt-10)
REVERT: B   59 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7418 (m-80)
REVERT: B  217 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7890 (ppp)
REVERT: G   47 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7421 (pt0)
REVERT: R   54 LEU cc_start: 0.7662 (tt) cc_final: 0.7461 (tp)
REVERT: R  140 ARG cc_start: 0.5969 (tpp80) cc_final: 0.5488 (tpt90)
REVERT: R  232 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5940 (mmtm)
REVERT: R  252 MET cc_start: 0.7282 (ttp) cc_final: 0.7053 (ttm)
REVERT: R  282 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6384 (tp)
REVERT: R  285 TYR cc_start: 0.6580 (t80) cc_final: 0.6078 (t80)
  outliers start: 32
  outliers final: 15
  residues processed: 131
  average time/residue: 1.1569
  time to fit residues: 161.3773
Evaluate side-chains
  121 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 58 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 237 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8457  Z= 0.256
  Angle     :  0.584   8.643  11471  Z= 0.307
  Chirality :  0.044   0.147   1304
  Planarity :  0.004   0.051   1460
  Dihedral  :  4.630  21.591   1152
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 14.52 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1041
  helix:  2.25 (0.25), residues: 399
  sheet:  0.65 (0.33), residues: 218
  loop : -0.89 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.016   0.002   PHE B 199 
 TYR   0.023   0.002   TYR R 148 
 ARG   0.008   0.001   ARG A 132 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5684 (mt-10)
REVERT: B  304 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7492 (mtm180)
REVERT: G   47 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7437 (pt0)
REVERT: N   79 LEU cc_start: 0.5539 (tp) cc_final: 0.5305 (tp)
REVERT: R   54 LEU cc_start: 0.7719 (tt) cc_final: 0.7510 (tp)
REVERT: R  140 ARG cc_start: 0.5982 (tpp80) cc_final: 0.5480 (tpt90)
REVERT: R  232 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5927 (mmtm)
REVERT: R  252 MET cc_start: 0.7374 (ttp) cc_final: 0.7109 (ttm)
REVERT: R  282 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6385 (tp)
  outliers start: 34
  outliers final: 16
  residues processed: 125
  average time/residue: 1.2640
  time to fit residues: 168.1396
Evaluate side-chains
  122 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 89 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0270
   chunk 85 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5838

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8457  Z= 0.164
  Angle     :  0.514   8.231  11471  Z= 0.268
  Chirality :  0.041   0.141   1304
  Planarity :  0.004   0.048   1460
  Dihedral  :  4.306  19.581   1152
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.36 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.52 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.26), residues: 1041
  helix:  2.64 (0.25), residues: 393
  sheet:  0.67 (0.32), residues: 221
  loop : -0.74 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 169 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.022   0.001   TYR R 148 
 ARG   0.009   0.000   ARG A 132 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5615 (mt-10)
REVERT: B   59 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7413 (m-80)
REVERT: G   47 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7419 (pt0)
REVERT: N   79 LEU cc_start: 0.5520 (tp) cc_final: 0.5301 (tp)
REVERT: R  140 ARG cc_start: 0.5956 (tpp80) cc_final: 0.5500 (tpt90)
REVERT: R  200 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6710 (t80)
REVERT: R  232 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5947 (mmtm)
REVERT: R  282 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6324 (tp)
  outliers start: 22
  outliers final: 13
  residues processed: 119
  average time/residue: 1.2662
  time to fit residues: 160.4381
Evaluate side-chains
  118 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  200 TYR
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0870
   chunk 96 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.6962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8457  Z= 0.182
  Angle     :  0.524   8.174  11471  Z= 0.274
  Chirality :  0.042   0.142   1304
  Planarity :  0.004   0.052   1460
  Dihedral  :  4.333  19.846   1152
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.55 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.41 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.26), residues: 1041
  helix:  2.65 (0.25), residues: 393
  sheet:  0.62 (0.32), residues: 218
  loop : -0.74 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.022   0.001   TYR R 148 
 ARG   0.011   0.000   ARG A 132 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 1.703 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5658 (mt-10)
REVERT: B   59 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7389 (m-80)
REVERT: B  197 ARG cc_start: 0.7124 (mmm-85) cc_final: 0.6842 (mmm-85)
REVERT: B  217 MET cc_start: 0.8185 (ppp) cc_final: 0.7875 (pmt)
REVERT: B  259 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7359 (mt0)
REVERT: G   47 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7417 (pt0)
REVERT: N   79 LEU cc_start: 0.5608 (tp) cc_final: 0.5399 (tp)
REVERT: R  140 ARG cc_start: 0.5945 (tpp80) cc_final: 0.5493 (tpt90)
REVERT: R  212 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7639 (mp)
REVERT: R  232 LYS cc_start: 0.6295 (OUTLIER) cc_final: 0.5954 (mmtm)
REVERT: R  282 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6525 (tt)
  outliers start: 24
  outliers final: 16
  residues processed: 121
  average time/residue: 1.3081
  time to fit residues: 168.7090
Evaluate side-chains
  122 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.0170
   chunk 93 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0370
   chunk 62 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.2102

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8457  Z= 0.246
  Angle     :  0.578   8.346  11471  Z= 0.303
  Chirality :  0.044   0.154   1304
  Planarity :  0.005   0.060   1460
  Dihedral  :  4.631  20.859   1152
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.13 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.08 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1041
  helix:  2.29 (0.25), residues: 399
  sheet:  0.57 (0.33), residues: 218
  loop : -0.84 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.016   0.002   PHE B 199 
 TYR   0.026   0.002   TYR R 148 
 ARG   0.011   0.001   ARG A 132 

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5686 (mt-10)
REVERT: B   59 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7539 (m-80)
REVERT: B  259 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7599 (mt0)
REVERT: G   47 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7435 (pt0)
REVERT: N   79 LEU cc_start: 0.5671 (tp) cc_final: 0.5400 (tp)
REVERT: R   54 LEU cc_start: 0.7673 (tt) cc_final: 0.7411 (tp)
REVERT: R  140 ARG cc_start: 0.6025 (tpp80) cc_final: 0.5540 (tpt90)
REVERT: R  212 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7683 (mp)
REVERT: R  232 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5971 (mmtm)
REVERT: R  282 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6538 (tt)
  outliers start: 26
  outliers final: 16
  residues processed: 117
  average time/residue: 1.2429
  time to fit residues: 154.6493
Evaluate side-chains
  119 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.189076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.152109 restraints weight = 8242.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 1.80
r_work: 0.3554 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8457  Z= 0.202
  Angle     :  0.549   8.255  11471  Z= 0.288
  Chirality :  0.042   0.147   1304
  Planarity :  0.004   0.054   1460
  Dihedral  :  4.493  20.154   1152
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.23 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.08 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.26), residues: 1041
  helix:  2.38 (0.25), residues: 399
  sheet:  0.55 (0.33), residues: 218
  loop : -0.83 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.012   0.000   ARG A 132 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3690.86 seconds
wall clock time: 65 minutes 13.17 seconds (3913.17 seconds total)