Starting phenix.real_space_refine
on Fri Jul 19 14:35:02 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/07_2024/8wst_37824.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/07_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_37824/07_2024/8wst_37824.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/07_2024/8wst_37824.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/07_2024/8wst_37824.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wst_37824/07_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-5388/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: 4.75, per 1000 atoms: 0.57
  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: 2.98
  Conformation dependent library (CDL) restraints added in 1.6 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: 0.94
  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: 2.55

  Time building geometry restraints manager: 3.28 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 2.440
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OH  TYR N  32 "
     model   vdw
     2.199 2.440
  nonbonded pdb=" O   LEU R 164 "
            pdb=" OH  TYR R 200 "
     model   vdw
     2.244 2.440
  nonbonded pdb=" O   PHE N  29 "
            pdb=" NH2 ARG N  72 "
     model   vdw
     2.264 2.520
  nonbonded pdb=" NH1 ARG B 283 "
            pdb=" OD1 ASP B 298 "
     model   vdw
     2.269 2.520
  ... (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
========== 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:             2.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.660
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.940
-------------------------------------------------------------------------------
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  : 0.892 
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: 1.2697
  time to fit residues: 265.5320
Evaluate side-chains
  112 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0770
   chunk 52 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.4476

-------------------------------------------------------------------------------
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 259 GLN
B 268 ASN
B 340 ASN
R 230 GLN
R 268 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2011

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= 0.152
  Angle     :  0.505   6.880  11471  Z= 0.261
  Chirality :  0.041   0.137   1304
  Planarity :  0.003   0.035   1460
  Dihedral  :  3.665  18.880   1152
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 10.98 %
    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:  2.15 (0.27), residues: 1041
  helix:  3.19 (0.27), residues: 387
  sheet:  1.23 (0.33), residues: 232
  loop : -0.17 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   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   0.006   0.000   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
  143 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5746 (mt-10)
REVERT: B   59 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7261 (m-80)
REVERT: N   49 SER cc_start: 0.7725 (p) cc_final: 0.7208 (t)
REVERT: R   98 GLU cc_start: 0.6228 (tt0) cc_final: 0.5970 (tt0)
REVERT: R  140 ARG cc_start: 0.5877 (tpp80) cc_final: 0.5382 (tpt90)
REVERT: R  247 MET cc_start: 0.5817 (mmm) cc_final: 0.5478 (mmt)
  outliers start: 27
  outliers final: 9
  residues processed: 131
  average time/residue: 1.1636
  time to fit residues: 162.7771
Evaluate side-chains
  117 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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  228 ASP
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:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0570
   chunk 91 optimal weight:    0.9980
   overall best weight:    1.1900

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
N 123 GLN
R 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8457  Z= 0.241
  Angle     :  0.585  11.098  11471  Z= 0.304
  Chirality :  0.044   0.145   1304
  Planarity :  0.004   0.038   1460
  Dihedral  :  4.361  20.317   1152
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 10.75 %
    Favored  : 85.81 %
  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:  1.56 (0.26), residues: 1041
  helix:  2.61 (0.26), residues: 393
  sheet:  0.88 (0.32), residues: 235
  loop : -0.43 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.007   0.002   HIS A 209 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.015   0.002   TYR A 191 
 ARG   0.004   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
  141 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5644 (mt-10)
REVERT: A   70 PHE cc_start: 0.6132 (t80) cc_final: 0.5787 (m-80)
REVERT: R   54 LEU cc_start: 0.7591 (tt) cc_final: 0.7384 (tp)
REVERT: R   98 GLU cc_start: 0.6249 (tt0) cc_final: 0.5978 (tt0)
REVERT: R  140 ARG cc_start: 0.5927 (tpp80) cc_final: 0.5399 (tpt90)
REVERT: R  232 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5736 (mmtm)
REVERT: R  247 MET cc_start: 0.5912 (mmm) cc_final: 0.5584 (mmt)
  outliers start: 31
  outliers final: 14
  residues processed: 128
  average time/residue: 1.3138
  time to fit residues: 178.0609
Evaluate side-chains
  112 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   52 THR
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:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3472

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= 0.239
  Angle     :  0.566   7.996  11471  Z= 0.298
  Chirality :  0.043   0.150   1304
  Planarity :  0.004   0.040   1460
  Dihedral  :  4.548  20.590   1152
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 11.20 %
    Favored  : 84.59 %
  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:  2.35 (0.26), residues: 393
  sheet:  0.74 (0.32), residues: 229
  loop : -0.66 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.015   0.002   PHE B 199 
 TYR   0.020   0.002   TYR A 191 
 ARG   0.006   0.001   ARG B  19 

*********************** 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: 38
    poor density    : 107
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5642 (mt-10)
REVERT: B  304 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7112 (mtm180)
REVERT: G   47 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7415 (pt0)
REVERT: N   79 LEU cc_start: 0.5486 (tp) cc_final: 0.5250 (tp)
REVERT: R   54 LEU cc_start: 0.7660 (tt) cc_final: 0.7441 (tp)
REVERT: R  140 ARG cc_start: 0.6022 (tpp80) cc_final: 0.5487 (tpt90)
REVERT: R  232 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5882 (mmtm)
REVERT: R  247 MET cc_start: 0.5857 (mmm) cc_final: 0.5564 (mmt)
REVERT: R  282 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6362 (tp)
  outliers start: 38
  outliers final: 18
  residues processed: 128
  average time/residue: 1.3015
  time to fit residues: 176.5077
Evaluate side-chains
  121 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
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  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
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 G residue   52 THR
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:    0.8980
   chunk 73 optimal weight:    0.0040
   chunk 40 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 88 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8457  Z= 0.161
  Angle     :  0.504   9.582  11471  Z= 0.262
  Chirality :  0.041   0.145   1304
  Planarity :  0.003   0.039   1460
  Dihedral  :  4.233  19.756   1152
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 13.75 %
    Favored  : 82.82 %
  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:  1.47 (0.26), residues: 1041
  helix:  2.73 (0.26), residues: 386
  sheet:  0.83 (0.32), residues: 228
  loop : -0.62 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.013   0.001   TYR A 191 
 ARG   0.003   0.000   ARG B  19 

*********************** 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
  137 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7624 (ttmm)
REVERT: A   28 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5574 (mt-10)
REVERT: R   54 LEU cc_start: 0.7668 (tt) cc_final: 0.7454 (tp)
REVERT: R   98 GLU cc_start: 0.6055 (tt0) cc_final: 0.5773 (tt0)
REVERT: R  140 ARG cc_start: 0.5904 (tpp80) cc_final: 0.5408 (tpt90)
REVERT: R  200 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6579 (t80)
REVERT: R  232 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5876 (mmtm)
REVERT: R  282 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6367 (tp)
  outliers start: 31
  outliers final: 18
  residues processed: 123
  average time/residue: 1.1872
  time to fit residues: 155.5723
Evaluate side-chains
  117 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  112 SER
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  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue   86 MET
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  225 TRP
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:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0970
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0010
   chunk 11 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8457  Z= 0.132
  Angle     :  0.473   8.735  11471  Z= 0.245
  Chirality :  0.040   0.140   1304
  Planarity :  0.003   0.038   1460
  Dihedral  :  4.038  19.009   1152
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.41 %
    Favored  : 82.59 %
  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:  1.62 (0.26), residues: 1041
  helix:  2.82 (0.26), residues: 393
  sheet:  0.87 (0.31), residues: 234
  loop : -0.55 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.013   0.001   TYR R 148 
 ARG   0.004   0.000   ARG B  19 

*********************** 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
  130 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5534 (mt-10)
REVERT: B   59 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7344 (m-80)
REVERT: G   47 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7392 (pt0)
REVERT: R   54 LEU cc_start: 0.7711 (tt) cc_final: 0.7505 (tp)
REVERT: R   98 GLU cc_start: 0.6100 (tt0) cc_final: 0.5827 (tt0)
REVERT: R  140 ARG cc_start: 0.5931 (tpp80) cc_final: 0.5448 (tpt90)
REVERT: R  195 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6613 (tm)
REVERT: R  200 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6450 (t80)
REVERT: R  225 TRP cc_start: 0.6781 (OUTLIER) cc_final: 0.6415 (t-100)
REVERT: R  232 LYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5964 (mmtm)
REVERT: R  247 MET cc_start: 0.5735 (mmm) cc_final: 0.5485 (mmt)
REVERT: R  282 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6336 (tp)
  outliers start: 27
  outliers final: 14
  residues processed: 119
  average time/residue: 1.1687
  time to fit residues: 148.1737
Evaluate side-chains
  117 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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  112 SER
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
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  148 TYR
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  200 TYR
Chi-restraints excluded: chain R residue  225 TRP
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:    0.6980
   chunk 55 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0020
   chunk 39 optimal weight:    0.1980
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.1792

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8457  Z= 0.225
  Angle     :  0.553   8.605  11471  Z= 0.290
  Chirality :  0.043   0.153   1304
  Planarity :  0.004   0.041   1460
  Dihedral  :  4.490  21.299   1152
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 14.63 %
    Favored  : 81.82 %
  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:  1.20 (0.26), residues: 1041
  helix:  2.39 (0.25), residues: 397
  sheet:  0.63 (0.32), residues: 232
  loop : -0.71 (0.30), residues: 412

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   0.015   0.002   PHE B 199 
 TYR   0.017   0.002   TYR A 191 
 ARG   0.003   0.000   ARG A  35 

*********************** 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
  137 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7637 (ttmm)
REVERT: A   28 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5648 (mt-10)
REVERT: G   47 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7405 (pt0)
REVERT: N   79 LEU cc_start: 0.5582 (tp) cc_final: 0.5343 (tp)
REVERT: R   54 LEU cc_start: 0.7717 (tt) cc_final: 0.7505 (tp)
REVERT: R  140 ARG cc_start: 0.6000 (tpp80) cc_final: 0.5481 (tpt90)
REVERT: R  195 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6594 (tm)
REVERT: R  200 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6806 (t80)
REVERT: R  232 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5889 (mmtm)
REVERT: R  282 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6485 (tp)
  outliers start: 32
  outliers final: 13
  residues processed: 124
  average time/residue: 1.2361
  time to fit residues: 163.4928
Evaluate side-chains
  117 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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  112 SER
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  247 ASP
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 66 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0570
   chunk 89 optimal weight:    9.9990
   chunk 94 optimal weight:    0.0070
   chunk 85 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0770
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3738

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= 0.132
  Angle     :  0.475   8.200  11471  Z= 0.248
  Chirality :  0.040   0.142   1304
  Planarity :  0.003   0.039   1460
  Dihedral  :  4.074  18.643   1152
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.46 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.41 %
    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:  1.55 (0.26), residues: 1041
  helix:  2.73 (0.26), residues: 396
  sheet:  0.86 (0.32), residues: 227
  loop : -0.57 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.022   0.001   TYR R 148 
 ARG   0.003   0.000   ARG B  19 

*********************** 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
  125 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5554 (mt-10)
REVERT: B   59 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7369 (m-80)
REVERT: G   47 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7368 (pt0)
REVERT: R  140 ARG cc_start: 0.5915 (tpp80) cc_final: 0.5440 (tpt90)
REVERT: R  195 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6614 (tm)
REVERT: R  200 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6503 (t80)
REVERT: R  232 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5913 (mmtm)
REVERT: R  247 MET cc_start: 0.5745 (mmm) cc_final: 0.5507 (mmt)
REVERT: R  282 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6335 (tp)
REVERT: R  285 TYR cc_start: 0.6438 (t80) cc_final: 0.5951 (t80)
  outliers start: 26
  outliers final: 13
  residues processed: 117
  average time/residue: 1.2487
  time to fit residues: 155.6608
Evaluate side-chains
  114 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
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   47 SER
Chi-restraints excluded: chain A residue  112 SER
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  247 ASP
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 G residue   52 THR
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  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:    0.1980
   chunk 71 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 96 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0970
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.3749

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= 0.146
  Angle     :  0.483   8.076  11471  Z= 0.252
  Chirality :  0.041   0.143   1304
  Planarity :  0.003   0.040   1460
  Dihedral  :  4.070  19.387   1152
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.75 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.85 %
    Favored  : 81.37 %
  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:  1.61 (0.27), residues: 1041
  helix:  2.76 (0.26), residues: 396
  sheet:  0.93 (0.32), residues: 227
  loop : -0.54 (0.31), residues: 418

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   0.027   0.001   TYR R 148 
 ARG   0.004   0.000   ARG B  19 

*********************** 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: 25
    poor density    : 102
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7726 (ttmm)
REVERT: A   28 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5548 (mt-10)
REVERT: B   59 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7340 (m-80)
REVERT: G   47 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7373 (pt0)
REVERT: R  140 ARG cc_start: 0.5957 (tpp80) cc_final: 0.5498 (tpt90)
REVERT: R  195 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6631 (tm)
REVERT: R  200 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6555 (t80)
REVERT: R  232 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5927 (mmtm)
REVERT: R  247 MET cc_start: 0.5733 (mmm) cc_final: 0.5503 (mmt)
REVERT: R  282 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6391 (tt)
REVERT: R  285 TYR cc_start: 0.6474 (t80) cc_final: 0.5903 (t80)
  outliers start: 25
  outliers final: 12
  residues processed: 120
  average time/residue: 1.2414
  time to fit residues: 158.3459
Evaluate side-chains
  116 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
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  112 SER
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  247 ASP
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 G residue   52 THR
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  195 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0030
   chunk 62 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8457  Z= 0.184
  Angle     :  0.518   7.964  11471  Z= 0.271
  Chirality :  0.042   0.153   1304
  Planarity :  0.004   0.041   1460
  Dihedral  :  4.284  20.162   1152
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.84 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.08 %
    Favored  : 81.26 %
  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:  1.41 (0.26), residues: 1041
  helix:  2.49 (0.26), residues: 402
  sheet:  0.83 (0.32), residues: 227
  loop : -0.60 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.026   0.001   TYR R 148 
 ARG   0.003   0.000   ARG B  19 

********************** 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
  121 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5634 (mt-10)
REVERT: B   59 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7432 (m-80)
REVERT: B  197 ARG cc_start: 0.7149 (mmm-85) cc_final: 0.6893 (mmm-85)
REVERT: G   47 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7402 (pt0)
REVERT: R   54 LEU cc_start: 0.7701 (tt) cc_final: 0.7486 (tt)
REVERT: R  140 ARG cc_start: 0.5992 (tpp80) cc_final: 0.5520 (tpt90)
REVERT: R  195 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6613 (tm)
REVERT: R  200 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6667 (t80)
REVERT: R  232 LYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5947 (mmtm)
REVERT: R  282 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6506 (tt)
  outliers start: 24
  outliers final: 15
  residues processed: 115
  average time/residue: 1.2739
  time to fit residues: 155.6227
Evaluate side-chains
  118 residues out of total 912 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
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  112 SER
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  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  247 ASP
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 G residue   52 THR
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  195 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.189311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.151312 restraints weight = 8206.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 1.80
r_work: 0.3544 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8457  Z= 0.210
  Angle     :  0.545   8.313  11471  Z= 0.286
  Chirality :  0.042   0.156   1304
  Planarity :  0.004   0.041   1460
  Dihedral  :  4.455  20.445   1152
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.13 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.41 %
    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:  1.30 (0.26), residues: 1041
  helix:  2.41 (0.26), residues: 397
  sheet:  0.75 (0.33), residues: 227
  loop : -0.61 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.023   0.002   TYR R 148 
 ARG   0.004   0.000   ARG B 214 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3625.59 seconds
wall clock time: 63 minutes 56.22 seconds (3836.22 seconds total)