Starting phenix.real_space_refine
on Sat Jun  7 08:49:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u4p_41890/06_2025/8u4p_41890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u4p_41890/06_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_41890/06_2025/8u4p_41890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u4p_41890/06_2025/8u4p_41890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u4p_41890/06_2025/8u4p_41890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u4p_41890/06_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-5710/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: 5.52, per 1000 atoms: 0.79
  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: 2.03
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.90
  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: 2.12

  Time building geometry restraints manager: 2.35 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.210
  Find NCS groups from input model:        0.080
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.860
-------------------------------------------------------------------------------
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   7159  Z= 0.176
  Angle     :  0.530   7.844   9709  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15820 (  365)
  hydrogen bonds       : angle       5.94274 ( 1062)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       1.06287 (    2)
  covalent geometry    : bond        0.00362 ( 7158)
  covalent geometry    : angle       0.53019 ( 9707)

*********************** 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  : 0.746 
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: 0.2221
  time to fit residues: 27.2784
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  : 0.764 
-------------------------------------------------------------------------------
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): 0.2938 rms_B_bonded: 2.29
r_work: 0.2769 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
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   7159  Z= 0.217
  Angle     :  0.581   6.153   9709  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06065 (  365)
  hydrogen bonds       : angle       4.83002 ( 1062)
  SS BOND              : bond        0.00205 (    1)
  SS BOND              : angle       2.06950 (    2)
  covalent geometry    : bond        0.00532 ( 7158)
  covalent geometry    : angle       0.58059 ( 9707)

*********************** 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  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7090 (tptt) cc_final: 0.6765 (tppt)
REVERT: A   53 MET cc_start: 0.2383 (ttt) cc_final: 0.2172 (ttt)
REVERT: B  154 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8678 (t0)
REVERT: B  290 ASP cc_start: 0.8659 (m-30) cc_final: 0.8411 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 96
  average time/residue: 0.2360
  time to fit residues: 29.0987
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  : 0.743 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   chunk 60 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.144477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105062 restraints weight = 7815.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.28
r_work: 0.2885 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7159  Z= 0.114
  Angle     :  0.473   6.042   9709  Z= 0.256
  Chirality :  0.040   0.140   1119
  Planarity :  0.003   0.035   1208
  Dihedral  :  4.734  29.846   1057
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  8.64 %
    Favored  : 89.74 %
  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:  0.80 (0.29), residues: 882
  helix:  2.06 (0.28), residues: 382
  sheet: -0.15 (0.38), residues: 179
  loop : -0.93 (0.33), residues: 321

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   0.010   0.001   TYR B  59 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  365)
  hydrogen bonds       : angle       4.53201 ( 1062)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       1.06507 (    2)
  covalent geometry    : bond        0.00247 ( 7158)
  covalent geometry    : angle       0.47235 ( 9707)

*********************** 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
  90 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7026 (tptt) cc_final: 0.6719 (tppt)
REVERT: B  154 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8712 (t0)
REVERT: B  290 ASP cc_start: 0.8617 (m-30) cc_final: 0.8325 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 88
  average time/residue: 0.2259
  time to fit residues: 25.9980
Evaluate side-chains
  81 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
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   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:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   chunk 78 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   chunk 19 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.4980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.149804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.108071 restraints weight = 7773.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.33
r_work: 0.2994 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7159  Z= 0.100
  Angle     :  0.447   5.856   9709  Z= 0.243
  Chirality :  0.040   0.140   1119
  Planarity :  0.003   0.035   1208
  Dihedral  :  4.465  28.418   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 :  1.48 %
    Allowed  : 10.12 %
    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:  1.00 (0.29), residues: 882
  helix:  2.17 (0.28), residues: 384
  sheet: -0.12 (0.38), residues: 181
  loop : -0.73 (0.34), residues: 317

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   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04109 (  365)
  hydrogen bonds       : angle       4.35780 ( 1062)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.75120 (    2)
  covalent geometry    : bond        0.00212 ( 7158)
  covalent geometry    : angle       0.44683 ( 9707)

*********************** 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
  89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.6925 (tptt) cc_final: 0.6634 (tppt)
REVERT: B  154 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8699 (t0)
REVERT: B  290 ASP cc_start: 0.8519 (m-30) cc_final: 0.8209 (m-30)
  outliers start: 11
  outliers final: 8
  residues processed: 89
  average time/residue: 0.2426
  time to fit residues: 27.9491
Evaluate side-chains
  82 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  234 PHE
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:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 82 optimal weight:    0.6980
   chunk 75 optimal weight:   30.0000
   chunk 5 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3603 r_free = 0.3603 target = 0.144640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.105169 restraints weight = 7805.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.29
r_work: 0.2887 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7159  Z= 0.115
  Angle     :  0.464   5.822   9709  Z= 0.250
  Chirality :  0.040   0.132   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.510  27.445   1057
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.39 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 882
  helix:  2.24 (0.28), residues: 384
  sheet: -0.16 (0.38), residues: 181
  loop : -0.73 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  79 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.007   0.001   TYR R 116 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04403 (  365)
  hydrogen bonds       : angle       4.35311 ( 1062)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.85958 (    2)
  covalent geometry    : bond        0.00260 ( 7158)
  covalent geometry    : angle       0.46366 ( 9707)

*********************** 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
  87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 1.302 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7090 (tptt) cc_final: 0.6764 (tppt)
REVERT: B  154 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8766 (t0)
REVERT: B  290 ASP cc_start: 0.8635 (m-30) cc_final: 0.8334 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2262
  time to fit residues: 25.5841
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  : 0.749 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 71 optimal weight:    0.1980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.142024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.100250 restraints weight = 7917.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.30
r_work: 0.2842 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7159  Z= 0.132
  Angle     :  0.478   5.921   9709  Z= 0.257
  Chirality :  0.041   0.132   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.615  27.226   1057
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.34 %
    Favored  : 86.64 %
  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 (0.29), residues: 882
  helix:  2.23 (0.28), residues: 384
  sheet: -0.22 (0.38), residues: 181
  loop : -0.76 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R  79 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.008   0.001   TYR A 320 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04677 (  365)
  hydrogen bonds       : angle       4.38793 ( 1062)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.94876 (    2)
  covalent geometry    : bond        0.00310 ( 7158)
  covalent geometry    : angle       0.47764 ( 9707)

*********************** 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
  87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7055 (tptt) cc_final: 0.6717 (tppt)
REVERT: B  154 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8761 (t0)
REVERT: B  290 ASP cc_start: 0.8611 (m-30) cc_final: 0.8305 (m-30)
  outliers start: 15
  outliers final: 13
  residues processed: 86
  average time/residue: 0.2228
  time to fit residues: 25.1062
Evaluate side-chains
  84 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.139804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.100293 restraints weight = 7855.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.29
r_work: 0.2760 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7159  Z= 0.201
  Angle     :  0.541   6.235   9709  Z= 0.289
  Chirality :  0.043   0.134   1119
  Planarity :  0.003   0.035   1208
  Dihedral  :  5.049  27.339   1057
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.15 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.29), residues: 882
  helix:  2.09 (0.28), residues: 383
  sheet: -0.43 (0.37), residues: 182
  loop : -0.79 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  63 
 HIS   0.006   0.001   HIS R  79 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.011   0.001   TYR A 320 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05664 (  365)
  hydrogen bonds       : angle       4.56993 ( 1062)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       1.29151 (    2)
  covalent geometry    : bond        0.00494 ( 7158)
  covalent geometry    : angle       0.54084 ( 9707)

*********************** 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
  92 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7156 (tptt) cc_final: 0.6872 (tppt)
REVERT: A  232 LEU cc_start: 0.7786 (mp) cc_final: 0.7524 (mp)
REVERT: B  118 ASP cc_start: 0.8397 (t0) cc_final: 0.8031 (t0)
REVERT: B  154 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8762 (t0)
REVERT: B  290 ASP cc_start: 0.8680 (m-30) cc_final: 0.8407 (m-30)
  outliers start: 16
  outliers final: 14
  residues processed: 91
  average time/residue: 0.2206
  time to fit residues: 26.6949
Evaluate side-chains
  86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0970
   chunk 5 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0970
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
B 259 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.147431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.105582 restraints weight = 7774.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.30
r_work: 0.2864 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7159  Z= 0.097
  Angle     :  0.446   6.059   9709  Z= 0.242
  Chirality :  0.040   0.141   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.454  27.458   1057
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.09 %
    Favored  : 85.16 %
  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:  1.00 (0.29), residues: 882
  helix:  2.28 (0.28), residues: 384
  sheet: -0.28 (0.38), residues: 181
  loop : -0.76 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  79 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.006   0.001   TYR R 116 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  365)
  hydrogen bonds       : angle       4.28438 ( 1062)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.63373 (    2)
  covalent geometry    : bond        0.00201 ( 7158)
  covalent geometry    : angle       0.44622 ( 9707)

*********************** 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
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.6969 (tptt) cc_final: 0.6663 (tppt)
REVERT: A  232 LEU cc_start: 0.7768 (mp) cc_final: 0.7523 (mp)
REVERT: B  154 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8770 (t0)
  outliers start: 13
  outliers final: 11
  residues processed: 88
  average time/residue: 0.2510
  time to fit residues: 29.3359
Evaluate side-chains
  85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    0.0020
   chunk 87 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0050
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.5604

-------------------------------------------------------------------------------
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 = 0.3613 r_free = 0.3613 target = 0.145554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.102996 restraints weight = 7837.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.35
r_work: 0.2865 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7159  Z= 0.105
  Angle     :  0.461   5.881   9709  Z= 0.248
  Chirality :  0.040   0.138   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.375  25.701   1057
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.50 %
    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:  1.10 (0.29), residues: 882
  helix:  2.36 (0.28), residues: 384
  sheet: -0.23 (0.38), residues: 181
  loop : -0.72 (0.33), residues: 317

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   0.013   0.001   PHE A 189 
 TYR   0.007   0.001   TYR R 116 
 ARG   0.005   0.000   ARG R  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04124 (  365)
  hydrogen bonds       : angle       4.24906 ( 1062)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.73656 (    2)
  covalent geometry    : bond        0.00228 ( 7158)
  covalent geometry    : angle       0.46135 ( 9707)

*********************** 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
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.6873 (tptt) cc_final: 0.6565 (tppt)
REVERT: A  232 LEU cc_start: 0.7649 (mp) cc_final: 0.7422 (mp)
REVERT: B  154 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8781 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 88
  average time/residue: 0.2307
  time to fit residues: 26.7237
Evaluate side-chains
  86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
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  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0040
   chunk 33 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.145441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.103973 restraints weight = 7912.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.38
r_work: 0.2884 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7159  Z= 0.111
  Angle     :  0.464   5.881   9709  Z= 0.251
  Chirality :  0.040   0.155   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.384  25.430   1057
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.90 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.29), residues: 882
  helix:  2.35 (0.28), residues: 384
  sheet: -0.25 (0.38), residues: 181
  loop : -0.72 (0.33), residues: 317

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   0.013   0.001   PHE A 189 
 TYR   0.007   0.001   TYR R 116 
 ARG   0.005   0.000   ARG R  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04202 (  365)
  hydrogen bonds       : angle       4.24296 ( 1062)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       0.77843 (    2)
  covalent geometry    : bond        0.00246 ( 7158)
  covalent geometry    : angle       0.46393 ( 9707)

********************** 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
  88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7039 (tptt) cc_final: 0.6714 (tppt)
REVERT: B  154 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (t0)
REVERT: B  290 ASP cc_start: 0.8620 (m-30) cc_final: 0.8319 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 88
  average time/residue: 0.2411
  time to fit residues: 27.8231
Evaluate side-chains
  86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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  322 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  131 SER
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    0.0670
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 13 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:
B  75 GLN
B 259 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.146991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.105214 restraints weight = 7803.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.30
r_work: 0.2870 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7159  Z= 0.114
  Angle     :  0.467   5.891   9709  Z= 0.252
  Chirality :  0.040   0.140   1119
  Planarity :  0.003   0.034   1208
  Dihedral  :  4.396  25.254   1057
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 14.04 %
    Favored  : 84.21 %
  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:  2.36 (0.28), residues: 384
  sheet: -0.23 (0.38), residues: 181
  loop : -0.71 (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   0.008   0.001   TYR B  59 
 ARG   0.005   0.000   ARG R  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04262 (  365)
  hydrogen bonds       : angle       4.25154 ( 1062)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.79039 (    2)
  covalent geometry    : bond        0.00253 ( 7158)
  covalent geometry    : angle       0.46641 ( 9707)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4508.87 seconds
wall clock time: 78 minutes 46.05 seconds (4726.05 seconds total)