Starting phenix.real_space_refine
on Wed Mar 12 19:36:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w89_37349/03_2025/8w89_37349.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w89_37349/03_2025/8w89_37349.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w89_37349/03_2025/8w89_37349.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w89_37349/03_2025/8w89_37349.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w89_37349/03_2025/8w89_37349.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w89_37349/03_2025/8w89_37349.cif"
  }
  resolution = 3.0
  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=   0.026
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      61      5.16       5
     C    5229      2.51       5
     N    1419      2.21       5
     O    1521      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8230
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1934
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2283
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 10
          Unusual residues: {'PEA': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 5.38, per 1000 atoms: 0.65
  Number of scatterers: 8230
  At special positions: 0
  Unit cell: (81.536, 100.672, 132.288, 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      61     16.00
     O    1521      8.00
     N    1419      7.00
     C    5229      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  96 " - pdb=" SG  CYS R 182 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      42.5% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 35
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 3.724A  pdb=" N   ILE A  56 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.735A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ASP A 102 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.188A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 3.650A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.617A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 20 through 52
      removed outlier: 4.354A  pdb=" N   LYS R  52 " --> pdb=" O   ILE R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 76
      removed outlier: 3.607A  pdb=" N   LEU R  61 " --> pdb=" O   PRO R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 85
    Processing helix  chain 'R' and resid 92 through 127
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 180
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 231
    Processing helix  chain 'R' and resid 247 through 274
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 275 through 279
      removed outlier: 4.137A  pdb=" N   HIS R 278 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR R 279 " --> pdb=" O   PHE R 276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 275 through 279'
    Processing helix  chain 'R' and resid 282 through 306
      removed outlier: 3.612A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP R 291 " --> pdb=" O   ASP R 287 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 316
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 3.632A  pdb=" N   PHE A  70 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.784A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.527A  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: 3.699A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.122A  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: 6.886A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.651A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.123A  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: 6.881A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.507A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.918A  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: 6.518A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
      removed outlier: 3.503A  pdb=" N   LEU N  18 " --> pdb=" O   MET N  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.548A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1233 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: 2.73

  Time building geometry restraints manager: 2.40 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1806
        1.33 -     1.46: 2217
        1.46 -     1.58: 4297
        1.58 -     1.71: 0
        1.71 -     1.84: 88
  Bond restraints: 8408
  Sorted by residual:
  bond pdb=" CA  TYR R 122 "
       pdb=" C   TYR R 122 "
    ideal  model  delta    sigma   weight residual
    1.524  1.471  0.053 1.27e-02 6.20e+03 1.75e+01
  bond pdb=" CA  ARG N  98 "
       pdb=" C   ARG N  98 "
    ideal  model  delta    sigma   weight residual
    1.526  1.474  0.052 1.37e-02 5.33e+03 1.43e+01
  bond pdb=" CA  THR A 216 "
       pdb=" C   THR A 216 "
    ideal  model  delta    sigma   weight residual
    1.523  1.481  0.042 1.21e-02 6.83e+03 1.18e+01
  bond pdb=" CA  TRP B 297 "
       pdb=" C   TRP B 297 "
    ideal  model  delta    sigma   weight residual
    1.523  1.485  0.039 1.18e-02 7.18e+03 1.07e+01
  bond pdb=" CA  ASN R 296 "
       pdb=" C   ASN R 296 "
    ideal  model  delta    sigma   weight residual
    1.524  1.482  0.041 1.29e-02 6.01e+03 1.02e+01
  ... (remaining 8403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 11015
        2.10 -     4.20: 297
        4.20 -     6.29: 64
        6.29 -     8.39: 7
        8.39 -    10.49: 5
  Bond angle restraints: 11388
  Sorted by residual:
  angle pdb=" N   GLN R  53 "
        pdb=" CA  GLN R  53 "
        pdb=" C   GLN R  53 "
      ideal   model   delta    sigma   weight residual
     113.38  104.99    8.39 1.23e+00 6.61e-01 4.65e+01
  angle pdb=" N   HIS R  50 "
        pdb=" CA  HIS R  50 "
        pdb=" C   HIS R  50 "
      ideal   model   delta    sigma   weight residual
     111.36  118.67   -7.31 1.09e+00 8.42e-01 4.50e+01
  angle pdb=" N   ARG R  23 "
        pdb=" CA  ARG R  23 "
        pdb=" C   ARG R  23 "
      ideal   model   delta    sigma   weight residual
     111.28  104.39    6.89 1.09e+00 8.42e-01 3.99e+01
  angle pdb=" N   GLN B 259 "
        pdb=" CA  GLN B 259 "
        pdb=" C   GLN B 259 "
      ideal   model   delta    sigma   weight residual
     109.14  117.78   -8.64 1.49e+00 4.50e-01 3.36e+01
  angle pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
        pdb=" C   ASP B 228 "
      ideal   model   delta    sigma   weight residual
     110.24  117.28   -7.04 1.47e+00 4.63e-01 2.29e+01
  ... (remaining 11383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 4545
       17.55 -    35.10: 367
       35.10 -    52.65: 68
       52.65 -    70.20: 12
       70.20 -    87.75: 5
  Dihedral angle restraints: 4997
    sinusoidal: 1957
      harmonic: 3040
  Sorted by residual:
  dihedral pdb=" N   ASP B 258 "
           pdb=" C   ASP B 258 "
           pdb=" CA  ASP B 258 "
           pdb=" CB  ASP B 258 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.20   -9.40     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.27   30.73     1      1.00e+01 1.00e-02 1.35e+01
  dihedral pdb=" C   VAL R 288 "
           pdb=" N   VAL R 288 "
           pdb=" CA  VAL R 288 "
           pdb=" CB  VAL R 288 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.56    8.56     0      2.50e+00 1.60e-01 1.17e+01
  ... (remaining 4994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1083
       0.076 -    0.152: 146
       0.152 -    0.229: 29
       0.229 -    0.305: 11
       0.305 -    0.381: 3
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  ASP B 258 "
            pdb=" N   ASP B 258 "
            pdb=" C   ASP B 258 "
            pdb=" CB  ASP B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  PHE R 268 "
            pdb=" N   PHE R 268 "
            pdb=" C   PHE R 268 "
            pdb=" CB  PHE R 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  TRP A  96 "
            pdb=" N   TRP A  96 "
            pdb=" C   TRP A  96 "
            pdb=" CB  TRP A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 1269 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  94 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.82e+00
        pdb=" C   VAL R  94 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   VAL R  94 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PHE R  95 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R  48 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.23e+00
        pdb=" C   ILE R  48 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ILE R  48 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER R  49 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R 265 "    0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO R 266 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO R 266 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R 266 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2856
        2.85 -     3.36: 7727
        3.36 -     3.87: 13913
        3.87 -     4.39: 16285
        4.39 -     4.90: 28042
  Nonbonded interactions: 68823
  Sorted by model distance:
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG1 THR R  37 "
            pdb=" OG1 THR R 298 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" O   SER R 115 "
            pdb=" OG  SER R 118 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" ND1 HIS B 311 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.430 3.120
  ... (remaining 68818 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8408  Z= 0.395
  Angle     :  0.826  10.489  11388  Z= 0.525
  Chirality :  0.063   0.381   1272
  Planarity :  0.005   0.067   1452
  Dihedral  : 13.331  87.748   3024
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  2.24 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1031
  helix:  2.05 (0.26), residues: 392
  sheet:  0.11 (0.36), residues: 216
  loop : -0.58 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  96 
 HIS   0.002   0.001   HIS R  63 
 PHE   0.023   0.002   PHE B 235 
 TYR   0.021   0.001   TYR A 210 
 ARG   0.005   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.928 
Fit side-chains
REVERT: B   34 THR cc_start: 0.8595 (p) cc_final: 0.8055 (p)
REVERT: B  175 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7335 (mp10)
REVERT: G   21 MET cc_start: 0.7482 (mtm) cc_final: 0.7240 (mmt)
REVERT: R  182 CYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4802 (p)
  outliers start: 8
  outliers final: 0
  residues processed: 163
  average time/residue: 1.1838
  time to fit residues: 205.5619
Evaluate side-chains
  131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  182 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    0.2980
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 223 ASN
B 220 GLN
B 259 GLN
R  53 GLN
R 175 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.161066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.127174 restraints weight = 10298.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.40
r_work: 0.3398 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8408  Z= 0.184
  Angle     :  0.541   6.825  11388  Z= 0.288
  Chirality :  0.043   0.318   1272
  Planarity :  0.004   0.047   1452
  Dihedral  :  4.507  57.269   1142
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.12 %
    Favored  : 86.42 %
  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:  1.07 (0.26), residues: 1031
  helix:  2.31 (0.26), residues: 396
  sheet:  0.20 (0.36), residues: 194
  loop : -0.53 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.018   0.001   PHE A  70 
 TYR   0.017   0.001   TYR A 210 
 ARG   0.005   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 THR cc_start: 0.8881 (p) cc_final: 0.8582 (p)
REVERT: B  101 MET cc_start: 0.8723 (mtp) cc_final: 0.8430 (mtp)
REVERT: B  153 ASP cc_start: 0.6778 (p0) cc_final: 0.6346 (m-30)
REVERT: B  175 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7446 (mp10)
REVERT: B  293 ASN cc_start: 0.7919 (m-40) cc_final: 0.7192 (p0)
REVERT: N   12 VAL cc_start: 0.8598 (p) cc_final: 0.8242 (m)
REVERT: R  143 MET cc_start: 0.7888 (mtt) cc_final: 0.7502 (mtm)
REVERT: R  166 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7523 (mptp)
REVERT: R  273 MET cc_start: 0.7600 (mmm) cc_final: 0.7340 (mmm)
  outliers start: 13
  outliers final: 6
  residues processed: 153
  average time/residue: 1.0976
  time to fit residues: 180.1040
Evaluate side-chains
  139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0670
   chunk 38 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 130 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.160413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.126730 restraints weight = 10576.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.45
r_work: 0.3394 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8408  Z= 0.178
  Angle     :  0.512   5.742  11388  Z= 0.274
  Chirality :  0.042   0.296   1272
  Planarity :  0.003   0.040   1452
  Dihedral  :  4.432  57.536   1142
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.37 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.07 (0.26), residues: 1031
  helix:  2.28 (0.25), residues: 396
  sheet:  0.16 (0.35), residues: 199
  loop : -0.47 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  87 
 PHE   0.040   0.001   PHE A  70 
 TYR   0.023   0.001   TYR R 172 
 ARG   0.004   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASN cc_start: 0.8715 (m110) cc_final: 0.8488 (m110)
REVERT: B  101 MET cc_start: 0.8706 (mtp) cc_final: 0.8405 (mtp)
REVERT: B  153 ASP cc_start: 0.6713 (p0) cc_final: 0.6278 (m-30)
REVERT: B  228 ASP cc_start: 0.8266 (m-30) cc_final: 0.8050 (m-30)
REVERT: B  269 ILE cc_start: 0.8452 (mm) cc_final: 0.8040 (mm)
REVERT: G   42 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6906 (mp0)
REVERT: N   12 VAL cc_start: 0.8563 (p) cc_final: 0.8186 (m)
REVERT: R  143 MET cc_start: 0.7909 (mtt) cc_final: 0.7552 (mtm)
REVERT: R  158 MET cc_start: 0.7240 (ttm) cc_final: 0.6733 (ttm)
REVERT: R  166 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7189 (mptp)
REVERT: R  207 LEU cc_start: 0.8619 (tp) cc_final: 0.8403 (tp)
  outliers start: 21
  outliers final: 8
  residues processed: 152
  average time/residue: 1.0912
  time to fit residues: 177.1680
Evaluate side-chains
  143 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
A 146 GLN
B  75 GLN
B 259 GLN
B 340 ASN
N 123 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.154300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119605 restraints weight = 10545.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.45
r_work: 0.3297 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.104   8408  Z= 0.427
  Angle     :  0.630   6.460  11388  Z= 0.336
  Chirality :  0.046   0.350   1272
  Planarity :  0.004   0.039   1452
  Dihedral  :  4.930  55.949   1142
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.82 %
    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:  0.72 (0.26), residues: 1031
  helix:  2.01 (0.25), residues: 397
  sheet: -0.23 (0.35), residues: 201
  loop : -0.58 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP N  47 
 HIS   0.007   0.001   HIS R  63 
 PHE   0.045   0.002   PHE A  70 
 TYR   0.031   0.002   TYR A 210 
 ARG   0.004   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 THR cc_start: 0.8326 (p) cc_final: 0.7864 (t)
REVERT: G   42 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7041 (mp0)
REVERT: N   12 VAL cc_start: 0.8610 (p) cc_final: 0.8200 (m)
REVERT: N   76 LYS cc_start: 0.8650 (mptt) cc_final: 0.8330 (mptt)
REVERT: N   77 ASN cc_start: 0.7165 (m-40) cc_final: 0.6603 (p0)
REVERT: R  166 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7262 (mptp)
  outliers start: 22
  outliers final: 7
  residues processed: 140
  average time/residue: 1.2008
  time to fit residues: 178.8320
Evaluate side-chains
  131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0370
   chunk 14 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
A 146 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.158814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124820 restraints weight = 10376.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.42
r_work: 0.3370 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8408  Z= 0.167
  Angle     :  0.523   6.823  11388  Z= 0.277
  Chirality :  0.041   0.212   1272
  Planarity :  0.003   0.038   1452
  Dihedral  :  4.596  57.367   1142
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.95 %
    Favored  : 81.03 %
  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:  0.95 (0.26), residues: 1031
  helix:  2.20 (0.26), residues: 399
  sheet: -0.15 (0.35), residues: 191
  loop : -0.44 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  87 
 PHE   0.037   0.001   PHE A  70 
 TYR   0.022   0.001   TYR R 172 
 ARG   0.004   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.795 
Fit side-chains
REVERT: A  157 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7664 (mtpt)
REVERT: B  101 MET cc_start: 0.8694 (mtp) cc_final: 0.8379 (mtp)
REVERT: B  269 ILE cc_start: 0.8474 (mm) cc_final: 0.8079 (mm)
REVERT: N   12 VAL cc_start: 0.8572 (p) cc_final: 0.8193 (m)
REVERT: N   77 ASN cc_start: 0.6980 (m-40) cc_final: 0.6679 (p0)
REVERT: R  166 LYS cc_start: 0.7382 (mmtt) cc_final: 0.7014 (mptp)
  outliers start: 18
  outliers final: 5
  residues processed: 146
  average time/residue: 1.1067
  time to fit residues: 172.6830
Evaluate side-chains
  133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    0.1980
   chunk 24 optimal weight:    9.9990
   chunk 55 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   chunk 23 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 146 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.159256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.125505 restraints weight = 10488.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.42
r_work: 0.3373 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8408  Z= 0.175
  Angle     :  0.540   9.125  11388  Z= 0.285
  Chirality :  0.042   0.359   1272
  Planarity :  0.003   0.040   1452
  Dihedral  :  4.478  57.531   1142
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.86 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1031
  helix:  2.11 (0.26), residues: 399
  sheet: -0.04 (0.35), residues: 186
  loop : -0.39 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 310 
 HIS   0.003   0.001   HIS R  87 
 PHE   0.033   0.001   PHE A  70 
 TYR   0.014   0.001   TYR N  80 
 ARG   0.004   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A  157 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7711 (mtpt)
REVERT: B  101 MET cc_start: 0.8685 (mtp) cc_final: 0.8393 (mtp)
REVERT: B  153 ASP cc_start: 0.6813 (p0) cc_final: 0.6432 (m-30)
REVERT: B  228 ASP cc_start: 0.8275 (m-30) cc_final: 0.8075 (m-30)
REVERT: B  234 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.8831 (m-80)
REVERT: G   42 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6956 (mp0)
REVERT: N   12 VAL cc_start: 0.8565 (p) cc_final: 0.8183 (m)
REVERT: N   76 LYS cc_start: 0.8531 (mptt) cc_final: 0.8172 (mptt)
REVERT: N   77 ASN cc_start: 0.6991 (m-40) cc_final: 0.6651 (p0)
REVERT: R   52 LYS cc_start: 0.7615 (mtmp) cc_final: 0.7351 (mtmm)
REVERT: R  158 MET cc_start: 0.7387 (ttm) cc_final: 0.6796 (ttm)
REVERT: R  166 LYS cc_start: 0.7266 (mmtt) cc_final: 0.6974 (mptp)
  outliers start: 17
  outliers final: 8
  residues processed: 138
  average time/residue: 1.4328
  time to fit residues: 211.2585
Evaluate side-chains
  135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
B  75 GLN
N 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.159166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.125185 restraints weight = 10502.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.43
r_work: 0.3371 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8408  Z= 0.185
  Angle     :  0.541  11.963  11388  Z= 0.285
  Chirality :  0.043   0.405   1272
  Planarity :  0.003   0.042   1452
  Dihedral  :  4.417  56.156   1142
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.52 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1031
  helix:  2.21 (0.26), residues: 393
  sheet: -0.00 (0.36), residues: 176
  loop : -0.41 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 310 
 HIS   0.003   0.001   HIS R  87 
 PHE   0.031   0.001   PHE A  70 
 TYR   0.016   0.001   TYR R 172 
 ARG   0.003   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ASN cc_start: 0.8701 (t0) cc_final: 0.8152 (m110)
REVERT: B  101 MET cc_start: 0.8775 (mtp) cc_final: 0.8537 (mtp)
REVERT: B  153 ASP cc_start: 0.6837 (p0) cc_final: 0.6428 (m-30)
REVERT: B  228 ASP cc_start: 0.8297 (m-30) cc_final: 0.8079 (m-30)
REVERT: G   17 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7276 (pp20)
REVERT: G   42 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7039 (mp0)
REVERT: N   12 VAL cc_start: 0.8542 (p) cc_final: 0.8166 (m)
REVERT: N   77 ASN cc_start: 0.6993 (m-40) cc_final: 0.6673 (p0)
REVERT: R   52 LYS cc_start: 0.7622 (mtmp) cc_final: 0.7331 (mtmm)
REVERT: R  158 MET cc_start: 0.7331 (ttm) cc_final: 0.6783 (ttm)
REVERT: R  166 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6953 (mptp)
REVERT: R  207 LEU cc_start: 0.8607 (tp) cc_final: 0.8400 (tp)
  outliers start: 16
  outliers final: 8
  residues processed: 142
  average time/residue: 1.1845
  time to fit residues: 179.5517
Evaluate side-chains
  138 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0870
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.4164

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 146 GLN
B  75 GLN
B 119 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.156762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122458 restraints weight = 10578.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.44
r_work: 0.3333 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8408  Z= 0.270
  Angle     :  0.585  11.879  11388  Z= 0.309
  Chirality :  0.044   0.411   1272
  Planarity :  0.004   0.044   1452
  Dihedral  :  4.585  53.915   1142
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.97 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1031
  helix:  1.99 (0.25), residues: 399
  sheet: -0.13 (0.35), residues: 187
  loop : -0.39 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP R 310 
 HIS   0.005   0.001   HIS R  63 
 PHE   0.031   0.002   PHE A  70 
 TYR   0.015   0.001   TYR R 172 
 ARG   0.003   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7623 (mtpt)
REVERT: B  153 ASP cc_start: 0.6859 (p0) cc_final: 0.6411 (m-30)
REVERT: B  176 GLN cc_start: 0.8970 (mt0) cc_final: 0.8753 (tt0)
REVERT: B  269 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8055 (mm)
REVERT: G   42 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7177 (mp0)
REVERT: N   12 VAL cc_start: 0.8516 (p) cc_final: 0.8090 (m)
REVERT: R  166 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6915 (mptp)
  outliers start: 20
  outliers final: 10
  residues processed: 137
  average time/residue: 1.1344
  time to fit residues: 165.7879
Evaluate side-chains
  132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Chi-restraints excluded: chain R residue  269 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.158148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.124011 restraints weight = 10663.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.47
r_work: 0.3356 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8408  Z= 0.204
  Angle     :  0.567  13.074  11388  Z= 0.297
  Chirality :  0.043   0.423   1272
  Planarity :  0.004   0.044   1452
  Dihedral  :  4.500  53.467   1142
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 19.53 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.26), residues: 1031
  helix:  2.04 (0.26), residues: 399
  sheet: -0.08 (0.36), residues: 174
  loop : -0.49 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP R 310 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.030   0.001   PHE A  70 
 TYR   0.014   0.001   TYR A 191 
 ARG   0.003   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7598 (mtpt)
REVERT: B  101 MET cc_start: 0.8781 (mtp) cc_final: 0.8489 (mtp)
REVERT: B  153 ASP cc_start: 0.6838 (p0) cc_final: 0.6425 (m-30)
REVERT: B  176 GLN cc_start: 0.8888 (mt0) cc_final: 0.8688 (tt0)
REVERT: B  269 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8161 (pp)
REVERT: G   42 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7155 (mp0)
REVERT: N    3 GLN cc_start: 0.7835 (pt0) cc_final: 0.7201 (tt0)
REVERT: N   12 VAL cc_start: 0.8509 (p) cc_final: 0.8104 (m)
REVERT: R  158 MET cc_start: 0.7446 (ttm) cc_final: 0.6847 (ttm)
REVERT: R  166 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6871 (mptp)
  outliers start: 16
  outliers final: 9
  residues processed: 138
  average time/residue: 1.1529
  time to fit residues: 169.6887
Evaluate side-chains
  131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
B  75 GLN
** N  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.158083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124321 restraints weight = 10399.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.42
r_work: 0.3361 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8408  Z= 0.244
  Angle     :  0.591  13.228  11388  Z= 0.311
  Chirality :  0.044   0.445   1272
  Planarity :  0.004   0.045   1452
  Dihedral  :  4.532  51.761   1142
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.75 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1031
  helix:  1.97 (0.26), residues: 399
  sheet: -0.22 (0.35), residues: 185
  loop : -0.43 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP R 310 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.047   0.002   PHE A  70 
 TYR   0.014   0.001   TYR A 191 
 ARG   0.003   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7575 (mtpt)
REVERT: B  101 MET cc_start: 0.8928 (mtp) cc_final: 0.8561 (mtp)
REVERT: B  153 ASP cc_start: 0.7036 (p0) cc_final: 0.6495 (m-30)
REVERT: B  228 ASP cc_start: 0.8351 (m-30) cc_final: 0.8109 (m-30)
REVERT: B  269 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7977 (pp)
REVERT: G   42 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7276 (mp0)
REVERT: N    3 GLN cc_start: 0.7802 (pt0) cc_final: 0.6967 (tt0)
REVERT: N   12 VAL cc_start: 0.8463 (p) cc_final: 0.8028 (m)
REVERT: R  162 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6977 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 133
  average time/residue: 1.1460
  time to fit residues: 162.4727
Evaluate side-chains
  133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 10 optimal weight:    0.3980
   chunk 97 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
B  75 GLN
N  77 ASN
N 123 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.160088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125548 restraints weight = 10603.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.48
r_work: 0.3377 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   8408  Z= 0.210
  Angle     :  0.579  13.972  11388  Z= 0.305
  Chirality :  0.044   0.428   1272
  Planarity :  0.004   0.045   1452
  Dihedral  :  4.466  51.632   1142
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 20.09 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1031
  helix:  1.98 (0.26), residues: 399
  sheet: -0.17 (0.36), residues: 174
  loop : -0.49 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP R 310 
 HIS   0.003   0.001   HIS R  87 
 PHE   0.045   0.001   PHE A  70 
 TYR   0.014   0.001   TYR A 191 
 ARG   0.003   0.000   ARG N  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5838.72 seconds
wall clock time: 101 minutes 29.52 seconds (6089.52 seconds total)