Starting phenix.real_space_refine
on Thu Feb 13 03:01:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u4p_41890/02_2025/8u4p_41890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u4p_41890/02_2025/8u4p_41890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u4p_41890/02_2025/8u4p_41890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u4p_41890/02_2025/8u4p_41890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u4p_41890/02_2025/8u4p_41890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u4p_41890/02_2025/8u4p_41890.cif"
  }
  resolution = 3.15
  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=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2008 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    4508      2.51       5
     N    1179      2.21       5
     O    1271      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7006
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1777
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2516
          Classifications: {'peptide': 335}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 49
    Chain: "C"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 345
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 2304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2304
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 9, 'TRANS': 276}
    Chain: "R"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 64
          Unusual residues: {'CLR': 1, 'VH6': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.59, per 1000 atoms: 0.66
  Number of scatterers: 7006
  At special positions: 0
  Unit cell: (73.1, 102, 130.9, 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      48     16.00
     O    1271      8.00
     N    1179      7.00
     C    4508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 109 " - pdb=" SG  CYS R 186 " 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: 1.85
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1690

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 9 sheets defined
      45.9% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.662A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.652A  pdb=" N   LYS A  51 " --> pdb=" O   CYS A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.501A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.526A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.641A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'R' and resid 34 through 65
      Proline residue:  R  42  - end of helix
    Processing helix  chain 'R' and resid 73 through 90
    Processing helix  chain 'R' and resid 90 through 100
      removed outlier: 4.186A  pdb=" N   TRP R  94 " --> pdb=" O   THR R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 106 through 140
      removed outlier: 3.789A  pdb=" N   VAL R 124 " --> pdb=" O   LEU R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 167
      removed outlier: 3.613A  pdb=" N   LYS R 149 " --> pdb=" O   GLN R 145 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   TYR R 157 " --> pdb=" O   GLU R 153 " (cutoff:3.500A)
      Proline residue:  R 163  - end of helix
    Processing helix  chain 'R' and resid 168 through 174
    Processing helix  chain 'R' and resid 192 through 208
      removed outlier: 3.682A  pdb=" N   VAL R 196 " --> pdb=" O   ASN R 192 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 227
      removed outlier: 3.669A  pdb=" N   LYS R 225 " --> pdb=" O   ILE R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 267
      removed outlier: 3.863A  pdb=" N   ALA R 237 " --> pdb=" O   GLN R 233 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LEU R 238 " --> pdb=" O   LYS R 234 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ILE R 243 " --> pdb=" O   LYS R 239 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU R 244 " --> pdb=" O   THR R 240 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU R 246 " --> pdb=" O   VAL R 242 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   CYS R 251 " --> pdb=" O   ALA R 247 " (cutoff:3.500A)
      Proline residue:  R 254  - end of helix
    Processing helix  chain 'R' and resid 273 through 292
      removed outlier: 3.670A  pdb=" N   GLU R 277 " --> pdb=" O   GLY R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 293 through 303
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 318
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.584A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.843A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.822A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.076A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.595A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 6.676A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.710A  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: 6.620A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.835A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 175 through 180
      removed outlier: 3.597A  pdb=" N   ASN R 176 " --> pdb=" O   ASP R 187 " (cutoff:3.500A)

    365 hydrogen bonds defined for protein.
    1062 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: 2.04

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2220
        1.34 -     1.46: 1251
        1.46 -     1.57: 3618
        1.57 -     1.69: 4
        1.69 -     1.81: 65
  Bond restraints: 7158
  Sorted by residual:
  bond pdb=" C22 VH6 R 702 "
       pdb=" N23 VH6 R 702 "
    ideal  model  delta    sigma   weight residual
    1.446  1.535 -0.089 2.00e-02 2.50e+03 1.99e+01
  bond pdb=" C24 VH6 R 702 "
       pdb=" N23 VH6 R 702 "
    ideal  model  delta    sigma   weight residual
    1.457  1.527 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C36 VH6 R 702 "
       pdb=" N23 VH6 R 702 "
    ideal  model  delta    sigma   weight residual
    1.455  1.520 -0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" C07 VH6 R 702 "
       pdb=" N08 VH6 R 702 "
    ideal  model  delta    sigma   weight residual
    1.455  1.513 -0.058 2.00e-02 2.50e+03 8.35e+00
  bond pdb=" C15 VH6 R 702 "
       pdb=" N08 VH6 R 702 "
    ideal  model  delta    sigma   weight residual
    1.456  1.513 -0.057 2.00e-02 2.50e+03 8.10e+00
  ... (remaining 7153 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 9518
        1.57 -     3.14: 149
        3.14 -     4.71: 25
        4.71 -     6.28: 12
        6.28 -     7.84: 3
  Bond angle restraints: 9707
  Sorted by residual:
  angle pdb=" C22 CLR R 701 "
        pdb=" C23 CLR R 701 "
        pdb=" C24 CLR R 701 "
      ideal   model   delta    sigma   weight residual
     111.95  104.11    7.84 3.00e+00 1.11e-01 6.84e+00
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  126.39   -4.85 1.91e+00 2.74e-01 6.45e+00
  angle pdb=" C24 VH6 R 702 "
        pdb=" N23 VH6 R 702 "
        pdb=" C36 VH6 R 702 "
      ideal   model   delta    sigma   weight residual
     115.20  107.60    7.60 3.00e+00 1.11e-01 6.42e+00
  angle pdb=" N   LEU R  91 "
        pdb=" CA  LEU R  91 "
        pdb=" C   LEU R  91 "
      ideal   model   delta    sigma   weight residual
     109.81  115.19   -5.38 2.21e+00 2.05e-01 5.94e+00
  angle pdb=" C   GLY R 159 "
        pdb=" N   VAL R 160 "
        pdb=" CA  VAL R 160 "
      ideal   model   delta    sigma   weight residual
     122.35  119.56    2.79 1.18e+00 7.18e-01 5.57e+00
  ... (remaining 9702 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 3860
       17.81 -    35.61: 358
       35.61 -    53.42: 64
       53.42 -    71.23: 5
       71.23 -    89.03: 9
  Dihedral angle restraints: 4296
    sinusoidal: 1690
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CB  GLU B 260 "
           pdb=" CG  GLU B 260 "
           pdb=" CD  GLU B 260 "
           pdb=" OE1 GLU B 260 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.03  -89.03     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU A 276 "
           pdb=" CG  GLU A 276 "
           pdb=" CD  GLU A 276 "
           pdb=" OE1 GLU A 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.27  -87.27     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CG  ARG B  22 "
           pdb=" CD  ARG B  22 "
           pdb=" NE  ARG B  22 "
           pdb=" CZ  ARG B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.41  -43.59     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 4293 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1016
       0.071 -    0.142: 99
       0.142 -    0.212: 0
       0.212 -    0.283: 1
       0.283 -    0.354: 3
  Chirality restraints: 1119
  Sorted by residual:
  chirality pdb=" C17 CLR R 701 "
            pdb=" C13 CLR R 701 "
            pdb=" C16 CLR R 701 "
            pdb=" C20 CLR R 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.35 2.00e-01 2.50e+01 3.13e+00
  chirality pdb=" C20 CLR R 701 "
            pdb=" C17 CLR R 701 "
            pdb=" C21 CLR R 701 "
            pdb=" C22 CLR R 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.90   -0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" C13 CLR R 701 "
            pdb=" C12 CLR R 701 "
            pdb=" C14 CLR R 701 "
            pdb=" C17 CLR R 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.23    0.29 2.00e-01 2.50e+01 2.15e+00
  ... (remaining 1116 not shown)

  Planarity restraints: 1208
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 152 "   -0.013 2.00e-02 2.50e+03   2.70e-02 7.28e+00
        pdb=" C   ALA R 152 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ALA R 152 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLU R 153 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 298 "   -0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO R 299 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO R 299 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO R 299 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 158 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.02e+00
        pdb=" C   VAL R 158 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   VAL R 158 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY R 159 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1205 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1206
        2.77 -     3.30: 6419
        3.30 -     3.84: 10965
        3.84 -     4.37: 12820
        4.37 -     4.90: 23460
  Nonbonded interactions: 54870
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG  SER A 293 "
            pdb=" OE1 GLU A 298 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.315 3.120
  ... (remaining 54865 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:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     19.650
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
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      :  0.004   0.089   7158  Z= 0.238
  Angle     :  0.530   7.844   9707  Z= 0.265
  Chirality :  0.044   0.354   1119
  Planarity :  0.003   0.036   1208
  Dihedral  : 14.369  89.035   2603
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.52 (0.29), residues: 882
  helix:  1.74 (0.28), residues: 381
  sheet: -0.17 (0.38), residues: 180
  loop : -1.02 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  79 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.008   0.001   TYR R 116 
 ARG   0.004   0.000   ARG R  70 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A   53 MET cc_start: 0.3392 (ttt) cc_final: 0.3191 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2216
  time to fit residues: 27.2382
Evaluate side-chains
  76 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** 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 = 0.3552 r_free = 0.3552 target = 0.140271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.098924 restraints weight = 7887.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 2.29
r_work: 0.2799 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7158  Z= 0.345
  Angle     :  0.581   6.153   9707  Z= 0.310
  Chirality :  0.044   0.138   1119
  Planarity :  0.004   0.037   1208
  Dihedral  :  5.161  26.909   1057
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  7.02 %
    Favored  : 91.50 %
  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:  0.56 (0.29), residues: 882
  helix:  1.80 (0.28), residues: 381
  sheet: -0.25 (0.38), residues: 178
  loop : -0.96 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  63 
 HIS   0.007   0.002   HIS R 203 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.012   0.001   TYR A 320 
 ARG   0.003   0.000   ARG R  70 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7104 (tptt) cc_final: 0.6777 (tppt)
REVERT: A   53 MET cc_start: 0.2394 (ttt) cc_final: 0.2186 (ttt)
REVERT: B  154 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8677 (t0)
REVERT: B  290 ASP cc_start: 0.8674 (m-30) cc_final: 0.8427 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 96
  average time/residue: 0.2391
  time to fit residues: 29.4487
Evaluate side-chains
  89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain R residue   53 ILE
Chi-restraints excluded: chain R residue  131 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0570
   chunk 10 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 195 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.145614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.105058 restraints weight = 7813.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 2.33
r_work: 0.2896 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7158  Z= 0.145
  Angle     :  0.462   6.029   9707  Z= 0.251
  Chirality :  0.040   0.140   1119
  Planarity :  0.003   0.035   1208
  Dihedral  :  4.679  30.156   1057
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.77 %
    Favored  : 89.88 %
  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 (0.29), residues: 882
  helix:  2.08 (0.28), residues: 383
  sheet: -0.13 (0.38), residues: 179
  loop : -0.88 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  79 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.007   0.000   ARG B 219 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7086 (tptt) cc_final: 0.6768 (tppt)
REVERT: A   53 MET cc_start: 0.2542 (ttt) cc_final: 0.2321 (ttt)
REVERT: B  154 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8721 (t0)
REVERT: B  290 ASP cc_start: 0.8641 (m-30) cc_final: 0.8349 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 87
  average time/residue: 0.2300
  time to fit residues: 26.4180
Evaluate side-chains
  83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    0.0270
   chunk 29 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.144805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.103308 restraints weight = 7845.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 2.29
r_work: 0.2906 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7158  Z= 0.158
  Angle     :  0.461   5.900   9707  Z= 0.249
  Chirality :  0.040   0.137   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.551  28.206   1057
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.72 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.29), residues: 882
  helix:  2.15 (0.28), residues: 384
  sheet: -0.17 (0.38), residues: 181
  loop : -0.75 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  79 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.007   0.001   TYR R 116 
 ARG   0.004   0.000   ARG R  70 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7034 (tptt) cc_final: 0.6718 (tppt)
REVERT: A   53 MET cc_start: 0.1907 (ttt) cc_final: 0.1678 (ttt)
REVERT: B  154 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8711 (t0)
REVERT: B  290 ASP cc_start: 0.8599 (m-30) cc_final: 0.8300 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 87
  average time/residue: 0.2275
  time to fit residues: 25.7575
Evaluate side-chains
  83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    0.0770
   chunk 58 optimal weight:    0.0370
   chunk 36 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 75 optimal weight:   30.0000
   chunk 5 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.146754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.104317 restraints weight = 7785.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.35
r_work: 0.2909 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7158  Z= 0.126
  Angle     :  0.439   5.815   9707  Z= 0.238
  Chirality :  0.039   0.137   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.375  27.797   1057
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.12 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 882
  helix:  2.31 (0.28), residues: 384
  sheet: -0.03 (0.38), residues: 179
  loop : -0.72 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  79 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.007   0.001   TYR R 116 
 ARG   0.007   0.000   ARG B 219 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.839 
Fit side-chains
REVERT: B  154 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8718 (t0)
REVERT: B  290 ASP cc_start: 0.8495 (m-30) cc_final: 0.8186 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 88
  average time/residue: 0.2254
  time to fit residues: 26.0929
Evaluate side-chains
  85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0980
   chunk 61 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 71 optimal weight:    0.2980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.146596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.104731 restraints weight = 7864.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.35
r_work: 0.2903 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7158  Z= 0.133
  Angle     :  0.445   5.748   9707  Z= 0.241
  Chirality :  0.040   0.134   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.332  26.876   1057
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.66 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.17 (0.29), residues: 882
  helix:  2.38 (0.28), residues: 384
  sheet: -0.03 (0.38), residues: 179
  loop : -0.72 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  79 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.007   0.001   TYR R 116 
 ARG   0.005   0.000   ARG B 219 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.771 
Fit side-chains
REVERT: B  154 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (t0)
REVERT: B  290 ASP cc_start: 0.8591 (m-30) cc_final: 0.8285 (m-30)
  outliers start: 14
  outliers final: 13
  residues processed: 91
  average time/residue: 0.2401
  time to fit residues: 28.4647
Evaluate side-chains
  87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0870
   chunk 49 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.3162

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.141716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.102124 restraints weight = 7845.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.30
r_work: 0.2846 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2689 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7158  Z= 0.262
  Angle     :  0.520   5.992   9707  Z= 0.279
  Chirality :  0.042   0.134   1119
  Planarity :  0.003   0.035   1208
  Dihedral  :  4.799  26.958   1057
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.42 %
    Favored  : 85.43 %
  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 (0.29), residues: 882
  helix:  2.23 (0.28), residues: 384
  sheet: -0.30 (0.38), residues: 182
  loop : -0.77 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  63 
 HIS   0.006   0.001   HIS R  79 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.009   0.001   TYR A 320 
 ARG   0.005   0.000   ARG B 219 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7128 (tptt) cc_final: 0.6787 (tppt)
REVERT: B  154 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8774 (t0)
REVERT: B  219 ARG cc_start: 0.8436 (mtt-85) cc_final: 0.8228 (mtt-85)
REVERT: B  290 ASP cc_start: 0.8683 (m-30) cc_final: 0.8404 (m-30)
  outliers start: 16
  outliers final: 13
  residues processed: 91
  average time/residue: 0.2313
  time to fit residues: 27.2269
Evaluate side-chains
  87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.101430 restraints weight = 7871.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 2.30
r_work: 0.2776 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7158  Z= 0.275
  Angle     :  0.522   6.180   9707  Z= 0.280
  Chirality :  0.042   0.134   1119
  Planarity :  0.003   0.035   1208
  Dihedral  :  4.884  27.327   1057
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 12.96 %
    Favored  : 84.62 %
  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 (0.29), residues: 882
  helix:  2.14 (0.28), residues: 384
  sheet: -0.41 (0.37), residues: 182
  loop : -0.78 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  63 
 HIS   0.006   0.001   HIS R  79 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.009   0.001   TYR A 320 
 ARG   0.005   0.000   ARG B 219 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7096 (tptt) cc_final: 0.6818 (tppt)
REVERT: B  154 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (t0)
REVERT: B  219 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.8217 (mtt-85)
REVERT: B  290 ASP cc_start: 0.8662 (m-30) cc_final: 0.8390 (m-30)
  outliers start: 18
  outliers final: 16
  residues processed: 90
  average time/residue: 0.2404
  time to fit residues: 27.8890
Evaluate side-chains
  89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   53 ILE
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 87 optimal weight:    0.1980
   chunk 44 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
B  75 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 = 0.3608 r_free = 0.3608 target = 0.145065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.102037 restraints weight = 7846.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.39
r_work: 0.2899 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7158  Z= 0.159
  Angle     :  0.470   6.057   9707  Z= 0.256
  Chirality :  0.040   0.139   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.511  26.949   1057
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.96 %
    Favored  : 84.75 %
  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:  1.05 (0.29), residues: 882
  helix:  2.29 (0.28), residues: 384
  sheet: -0.25 (0.38), residues: 181
  loop : -0.70 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  79 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.006   0.001   TYR R 116 
 ARG   0.005   0.000   ARG B 219 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.6923 (tptt) cc_final: 0.6608 (tppt)
REVERT: A  232 LEU cc_start: 0.7821 (mp) cc_final: 0.7591 (mp)
REVERT: B  154 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8760 (t0)
REVERT: B  219 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.8173 (mtt-85)
REVERT: B  290 ASP cc_start: 0.8581 (m-30) cc_final: 0.8277 (m-30)
  outliers start: 17
  outliers final: 16
  residues processed: 92
  average time/residue: 0.2397
  time to fit residues: 28.4611
Evaluate side-chains
  90 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   53 ILE
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0980
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.145706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.103998 restraints weight = 7907.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.39
r_work: 0.2853 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7158  Z= 0.155
  Angle     :  0.470   5.932   9707  Z= 0.255
  Chirality :  0.040   0.141   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.429  25.773   1057
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.09 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 882
  helix:  2.34 (0.28), residues: 384
  sheet: -0.20 (0.38), residues: 181
  loop : -0.66 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  79 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.007   0.001   TYR R 116 
 ARG   0.005   0.000   ARG R  70 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.6984 (tptt) cc_final: 0.6665 (tppt)
REVERT: B  154 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8799 (t0)
REVERT: B  219 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.8210 (mtt-85)
  outliers start: 17
  outliers final: 16
  residues processed: 88
  average time/residue: 0.2499
  time to fit residues: 28.5176
Evaluate side-chains
  89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   53 ILE
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.146335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.105508 restraints weight = 7808.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.37
r_work: 0.2866 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7158  Z= 0.180
  Angle     :  0.482   5.960   9707  Z= 0.261
  Chirality :  0.041   0.151   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.473  25.457   1057
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.09 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.29), residues: 882
  helix:  2.34 (0.28), residues: 384
  sheet: -0.26 (0.38), residues: 182
  loop : -0.66 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  79 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R  70 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4152.60 seconds
wall clock time: 74 minutes 9.76 seconds (4449.76 seconds total)