Starting phenix.real_space_refine
on Tue Feb 11 23:35:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xbw_33107/02_2025/7xbw_33107.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xbw_33107/02_2025/7xbw_33107.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xbw_33107/02_2025/7xbw_33107.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xbw_33107/02_2025/7xbw_33107.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xbw_33107/02_2025/7xbw_33107.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xbw_33107/02_2025/7xbw_33107.cif"
  }
  resolution = 2.8
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4316      2.51       5
     N    1087      2.21       5
     O    1218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 6663
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1657
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2394
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 109
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 93
    Chain: "E"
      Number of atoms: 352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 352
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "R"
      Number of atoms: 2176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2176
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 9, 'TRANS': 278}
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 198
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 105
    Chain: "R"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 84
          Unusual residues: {'CLR': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.98, per 1000 atoms: 0.60
  Number of scatterers: 6663
  At special positions: 0
  Unit cell: (107.635, 111.815, 73.15, 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      42     16.00
     O    1218      8.00
     N    1087      7.00
     C    4316      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 175 " 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: 1.81
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1676

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      45.4% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'C' and resid 6 through 32
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 4.348A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.593A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 230
      No H-bonds generated for 'chain 'C' and resid 228 through 230'
    Processing helix  chain 'C' and resid 242 through 255
    Processing helix  chain 'C' and resid 270 through 281
      removed outlier: 4.063A  pdb=" N   GLU C 276 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 309
    Processing helix  chain 'C' and resid 327 through 349
      removed outlier: 4.333A  pdb=" N   ASN C 331 " --> pdb=" O   THR C 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 26
    Processing helix  chain 'D' and resid 29 through 34
    Processing helix  chain 'E' and resid 10 through 25
      removed outlier: 3.686A  pdb=" N   GLU E  17 " --> pdb=" O   ARG E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 44
    Processing helix  chain 'E' and resid 45 through 48
    Processing helix  chain 'R' and resid 30 through 57
    Processing helix  chain 'R' and resid 64 through 92
      Proline residue:  R  85  - end of helix
    Processing helix  chain 'R' and resid 98 through 132
    Processing helix  chain 'R' and resid 133 through 140
    Processing helix  chain 'R' and resid 145 through 162
      removed outlier: 3.637A  pdb=" N   ILE R 149 " --> pdb=" O   HIS R 145 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 163 through 165
      No H-bonds generated for 'chain 'R' and resid 163 through 165'
    Processing helix  chain 'R' and resid 180 through 185
      removed outlier: 3.838A  pdb=" N   GLU R 185 " --> pdb=" O   GLU R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 186 through 201
    Processing helix  chain 'R' and resid 201 through 221
      removed outlier: 3.503A  pdb=" N   LEU R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 227 through 259
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 266 through 289
      removed outlier: 5.433A  pdb=" N   ARG R 272 " --> pdb=" O   ARG R 268 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   LEU R 273 " --> pdb=" O   LYS R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 291 through 297
      removed outlier: 3.960A  pdb=" N   PHE R 295 " --> pdb=" O   LEU R 291 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 297 through 310
      removed outlier: 3.746A  pdb=" N   LYS R 310 " --> pdb=" O   HIS R 306 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 55
      removed outlier: 6.418A  pdb=" N   HIS C 188 " --> pdb=" O   LYS C  54 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL C 185 " --> pdb=" O   ASP C 200 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   LEU C  39 " --> pdb=" O   CYS C 224 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   ALA C 226 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63
      removed outlier: 3.737A  pdb=" N   ALA D  60 " --> pdb=" O   ALA D  73 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE D  80 " --> pdb=" O   SER D  72 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ILE D  81 " --> pdb=" O   VAL D  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 103 through 105
      removed outlier: 5.823A  pdb=" N   CYS D 121 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU D 138 " --> pdb=" O   CYS D 121 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE D 123 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG D 134 " --> pdb=" O   ASN D 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151
      removed outlier: 3.678A  pdb=" N   THR D 178 " --> pdb=" O   LEU D 168 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ASP D 170 " --> pdb=" O   GLN D 176 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN D 176 " --> pdb=" O   ASP D 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192
      removed outlier: 6.973A  pdb=" N   GLY D 202 " --> pdb=" O   MET D 188 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LEU D 190 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL D 200 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   LEU D 192 " --> pdb=" O   LEU D 198 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   LEU D 198 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER D 201 " --> pdb=" O   LYS D 209 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS D 209 " --> pdb=" O   SER D 201 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ALA D 203 " --> pdb=" O   SER D 207 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   SER D 207 " --> pdb=" O   ALA D 203 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLN D 220 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   ASP D 212 " --> pdb=" O   CYS D 218 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   CYS D 218 " --> pdb=" O   ASP D 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234
      removed outlier: 3.776A  pdb=" N   MET D 262 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   ASP D 254 " --> pdb=" O   GLU D 260 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLU D 260 " --> pdb=" O   ASP D 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278
      removed outlier: 6.943A  pdb=" N   VAL D 296 " --> pdb=" O   ALA D 305 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1065 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: 1.73

  Time building geometry restraints manager: 2.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2115
        1.34 -     1.46: 1643
        1.46 -     1.58: 2993
        1.58 -     1.70: 4
        1.70 -     1.81: 55
  Bond restraints: 6810
  Sorted by residual:
  bond pdb=" C5  CLR R 403 "
       pdb=" C6  CLR R 403 "
    ideal  model  delta    sigma   weight residual
    1.332  1.465 -0.133 2.00e-02 2.50e+03 4.40e+01
  bond pdb=" C5  CLR R 401 "
       pdb=" C6  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.464 -0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" C5  CLR R 402 "
       pdb=" C6  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.463 -0.131 2.00e-02 2.50e+03 4.31e+01
  bond pdb=" C3  CLR R 402 "
       pdb=" O1  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.413  1.298  0.115 2.00e-02 2.50e+03 3.28e+01
  bond pdb=" C3  CLR R 401 "
       pdb=" O1  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.413  1.299  0.114 2.00e-02 2.50e+03 3.23e+01
  ... (remaining 6805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 9145
        1.73 -     3.45: 123
        3.45 -     5.18: 36
        5.18 -     6.90: 7
        6.90 -     8.63: 1
  Bond angle restraints: 9312
  Sorted by residual:
  angle pdb=" CA  PRO E  60 "
        pdb=" N   PRO E  60 "
        pdb=" CD  PRO E  60 "
      ideal   model   delta    sigma   weight residual
     112.00  106.71    5.29 1.40e+00 5.10e-01 1.43e+01
  angle pdb=" C   TYR R 259 "
        pdb=" N   ASP R 260 "
        pdb=" CA  ASP R 260 "
      ideal   model   delta    sigma   weight residual
     122.08  125.76   -3.68 1.47e+00 4.63e-01 6.27e+00
  angle pdb=" CA  LEU R  84 "
        pdb=" CB  LEU R  84 "
        pdb=" CG  LEU R  84 "
      ideal   model   delta    sigma   weight residual
     116.30  124.93   -8.63 3.50e+00 8.16e-02 6.08e+00
  angle pdb=" C   PRO E  60 "
        pdb=" CA  PRO E  60 "
        pdb=" CB  PRO E  60 "
      ideal   model   delta    sigma   weight residual
     110.00  112.72   -2.72 1.12e+00 7.97e-01 5.92e+00
  angle pdb=" C   PRO C 282 "
        pdb=" N   LEU C 283 "
        pdb=" CA  LEU C 283 "
      ideal   model   delta    sigma   weight residual
     121.54  126.14   -4.60 1.91e+00 2.74e-01 5.81e+00
  ... (remaining 9307 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.96: 3718
       14.96 -    29.91: 286
       29.91 -    44.87: 82
       44.87 -    59.82: 8
       59.82 -    74.78: 4
  Dihedral angle restraints: 4098
    sinusoidal: 1515
      harmonic: 2583
  Sorted by residual:
  dihedral pdb=" CA  ASP D 170 "
           pdb=" CB  ASP D 170 "
           pdb=" CG  ASP D 170 "
           pdb=" OD1 ASP D 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.40   51.40     1      2.00e+01 2.50e-03 9.03e+00
  dihedral pdb=" CA  CYS R 102 "
           pdb=" CB  CYS R 102 "
           pdb=" SG  CYS R 102 "
           pdb=" SG  CYS R 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00  129.88  -50.88     1      2.00e+01 2.50e-03 8.86e+00
  dihedral pdb=" CB  ARG D 150 "
           pdb=" CG  ARG D 150 "
           pdb=" CD  ARG D 150 "
           pdb=" NE  ARG D 150 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  106.56  -46.56     3      1.50e+01 4.44e-03 8.35e+00
  ... (remaining 4095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 858
       0.043 -    0.087: 202
       0.087 -    0.130: 59
       0.130 -    0.173: 5
       0.173 -    0.217: 3
  Chirality restraints: 1127
  Sorted by residual:
  chirality pdb=" C14 CLR R 403 "
            pdb=" C13 CLR R 403 "
            pdb=" C15 CLR R 403 "
            pdb=" C8  CLR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.53    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" C14 CLR R 401 "
            pdb=" C13 CLR R 401 "
            pdb=" C15 CLR R 401 "
            pdb=" C8  CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.52    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C14 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C15 CLR R 402 "
            pdb=" C8  CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.52    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1124 not shown)

  Planarity restraints: 1155
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  38 "    0.053 5.00e-02 4.00e+02   8.07e-02 1.04e+01
        pdb=" N   PRO D  39 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO D  39 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D  39 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E  59 "    0.039 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO E  60 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO E  60 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO E  60 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  84 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.33e+00
        pdb=" N   PRO R  85 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO R  85 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R  85 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1152 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1388
        2.78 -     3.31: 6610
        3.31 -     3.84: 11485
        3.84 -     4.37: 13225
        4.37 -     4.90: 23050
  Nonbonded interactions: 55758
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 274 "
            pdb=" O   VAL D 315 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OH  TYR R 179 "
            pdb=" NH1 ARG R 191 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OG1 THR D  86 "
            pdb=" OD1 ASN D  88 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OD2 ASP C 200 "
            pdb=" OG1 THR C 202 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR D 145 "
            pdb=" OD2 ASP D 186 "
     model   vdw
     2.288 3.040
  ... (remaining 55753 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.760
  Find NCS groups from input model:        0.070
  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:13.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
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      :  0.005   0.133   6810  Z= 0.286
  Angle     :  0.542   8.631   9312  Z= 0.271
  Chirality :  0.042   0.217   1127
  Planarity :  0.004   0.081   1155
  Dihedral  : 11.689  74.778   2419
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  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:  1.47 (0.30), residues: 874
  helix:  2.46 (0.27), residues: 382
  sheet:  0.54 (0.41), residues: 178
  loop : -0.64 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  82 
 HIS   0.004   0.001   HIS R 285 
 PHE   0.020   0.001   PHE R 110 
 TYR   0.019   0.001   TYR R  90 
 ARG   0.004   0.000   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.675 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 1.0712
  time to fit residues: 133.7281
Evaluate side-chains
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 50 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
R 170 GLN
R 248 ASN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.187215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.142183 restraints weight = 6730.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.59
r_work: 0.3557 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6810  Z= 0.272
  Angle     :  0.566   8.856   9312  Z= 0.295
  Chirality :  0.042   0.143   1127
  Planarity :  0.004   0.061   1155
  Dihedral  :  4.517  52.652   1125
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.86 %
    Favored  : 85.02 %
  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:  1.21 (0.29), residues: 874
  helix:  2.13 (0.26), residues: 387
  sheet:  0.30 (0.39), residues: 183
  loop : -0.60 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  82 
 HIS   0.007   0.001   HIS R 285 
 PHE   0.025   0.002   PHE R 110 
 TYR   0.014   0.002   TYR D  59 
 ARG   0.004   0.000   ARG C  15 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.679 
Fit side-chains
REVERT: C    9 ASP cc_start: 0.6579 (m-30) cc_final: 0.6348 (OUTLIER)
REVERT: C  313 ARG cc_start: 0.7375 (mtt90) cc_final: 0.7088 (mtt90)
REVERT: D   52 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.8075 (mtt90)
REVERT: D  134 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7728 (ptp-110)
REVERT: D  304 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7539 (mtm110)
REVERT: R  288 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6100 (pt)
  outliers start: 14
  outliers final: 8
  residues processed: 113
  average time/residue: 1.0899
  time to fit residues: 130.4116
Evaluate side-chains
  104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 188 HIS
** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 223 ASN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.185169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.136688 restraints weight = 6812.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.14
r_work: 0.3532 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6810  Z= 0.217
  Angle     :  0.526   8.118   9312  Z= 0.276
  Chirality :  0.040   0.137   1127
  Planarity :  0.003   0.053   1155
  Dihedral  :  4.522  50.339   1125
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.19 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 874
  helix:  1.99 (0.26), residues: 392
  sheet:  0.10 (0.39), residues: 175
  loop : -0.63 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 
 PHE   0.023   0.002   PHE R 110 
 TYR   0.021   0.001   TYR R  90 
 ARG   0.003   0.000   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.674 
Fit side-chains
REVERT: C  198 MET cc_start: 0.8782 (mpp) cc_final: 0.8246 (mpp)
REVERT: C  306 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7559 (mt0)
REVERT: D  196 THR cc_start: 0.6805 (m) cc_final: 0.6510 (p)
REVERT: R  288 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6297 (pt)
  outliers start: 14
  outliers final: 6
  residues processed: 124
  average time/residue: 1.0067
  time to fit residues: 132.7733
Evaluate side-chains
  106 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 164 GLN
R 306 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.180979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.138074 restraints weight = 7024.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.98
r_work: 0.3430 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6810  Z= 0.233
  Angle     :  0.550  11.514   9312  Z= 0.284
  Chirality :  0.040   0.137   1127
  Planarity :  0.003   0.049   1155
  Dihedral  :  4.600  58.040   1125
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 18.61 %
    Favored  : 77.00 %
  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:  0.97 (0.28), residues: 874
  helix:  2.01 (0.26), residues: 387
  sheet: -0.07 (0.37), residues: 182
  loop : -0.64 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  82 
 HIS   0.008   0.001   HIS R 285 
 PHE   0.024   0.002   PHE R 110 
 TYR   0.021   0.001   TYR R  90 
 ARG   0.003   0.000   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.687 
Fit side-chains
REVERT: C  309 ASP cc_start: 0.7496 (m-30) cc_final: 0.7180 (m-30)
REVERT: D  212 ASP cc_start: 0.7969 (t0) cc_final: 0.7743 (t0)
REVERT: D  270 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7651 (pp)
REVERT: D  304 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7653 (mtt90)
REVERT: R  288 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6340 (pt)
  outliers start: 29
  outliers final: 15
  residues processed: 128
  average time/residue: 0.9603
  time to fit residues: 131.2250
Evaluate side-chains
  117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  304 ARG
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    0.0050
   chunk 77 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
D 340 ASN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 164 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.181659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.140367 restraints weight = 6916.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.95
r_work: 0.3459 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6810  Z= 0.197
  Angle     :  0.539  10.367   9312  Z= 0.279
  Chirality :  0.040   0.135   1127
  Planarity :  0.003   0.046   1155
  Dihedral  :  4.428  53.019   1125
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 19.52 %
    Favored  : 76.25 %
  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:  0.94 (0.28), residues: 874
  helix:  2.05 (0.26), residues: 387
  sheet: -0.12 (0.37), residues: 180
  loop : -0.72 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 
 PHE   0.024   0.001   PHE R 165 
 TYR   0.021   0.001   TYR R  90 
 ARG   0.006   0.000   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.704 
Fit side-chains
REVERT: D   46 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7221 (mmm160)
REVERT: D  263 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8436 (m)
REVERT: D  304 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7654 (mtt90)
REVERT: R  288 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6384 (pt)
  outliers start: 28
  outliers final: 14
  residues processed: 118
  average time/residue: 0.9407
  time to fit residues: 118.4432
Evaluate side-chains
  112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  304 ARG
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  164 GLN
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 164 GLN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.178242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.135425 restraints weight = 6949.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 1.96
r_work: 0.3472 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6810  Z= 0.267
  Angle     :  0.583   9.601   9312  Z= 0.301
  Chirality :  0.041   0.137   1127
  Planarity :  0.003   0.044   1155
  Dihedral  :  4.577  48.589   1125
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 20.27 %
    Favored  : 75.64 %
  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:  0.91 (0.28), residues: 874
  helix:  1.96 (0.26), residues: 387
  sheet: -0.07 (0.37), residues: 186
  loop : -0.70 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  82 
 HIS   0.008   0.001   HIS R 285 
 PHE   0.024   0.002   PHE R 165 
 TYR   0.023   0.001   TYR R  90 
 ARG   0.006   0.000   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.667 
Fit side-chains
REVERT: C  276 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6807 (pm20)
REVERT: C  309 ASP cc_start: 0.7616 (m-30) cc_final: 0.7315 (m-30)
REVERT: D   46 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7413 (mmm160)
REVERT: D  270 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7766 (pp)
REVERT: D  304 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7706 (mtt90)
REVERT: R  164 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.5915 (mp-120)
REVERT: R  288 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6434 (pt)
  outliers start: 27
  outliers final: 16
  residues processed: 129
  average time/residue: 0.9725
  time to fit residues: 134.1194
Evaluate side-chains
  119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  304 ARG
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  164 GLN
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 164 GLN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.178184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.135671 restraints weight = 6946.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.96
r_work: 0.3392 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6810  Z= 0.242
  Angle     :  0.582  11.981   9312  Z= 0.300
  Chirality :  0.041   0.134   1127
  Planarity :  0.003   0.043   1155
  Dihedral  :  4.594  49.745   1125
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 20.88 %
    Favored  : 74.74 %
  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:  0.81 (0.28), residues: 874
  helix:  1.89 (0.26), residues: 391
  sheet: -0.06 (0.38), residues: 174
  loop : -0.83 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 
 PHE   0.029   0.002   PHE R 165 
 TYR   0.024   0.001   TYR R  90 
 ARG   0.008   0.001   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.676 
Fit side-chains
REVERT: C  251 ASP cc_start: 0.8310 (t0) cc_final: 0.8106 (t0)
REVERT: C  276 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6804 (pm20)
REVERT: D   46 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7475 (mmm160)
REVERT: D  270 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7780 (pp)
REVERT: R  103 LYS cc_start: 0.6785 (ttmm) cc_final: 0.6463 (mmtm)
REVERT: R  171 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6389 (ptpp)
REVERT: R  288 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6523 (pt)
  outliers start: 29
  outliers final: 18
  residues processed: 118
  average time/residue: 0.9993
  time to fit residues: 125.3799
Evaluate side-chains
  120 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  171 LYS
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    0.0670
   chunk 8 optimal weight:    0.3980
   chunk 40 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 164 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.181493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.135587 restraints weight = 6930.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.05
r_work: 0.3526 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6810  Z= 0.176
  Angle     :  0.549  11.767   9312  Z= 0.284
  Chirality :  0.040   0.132   1127
  Planarity :  0.003   0.043   1155
  Dihedral  :  4.444  52.539   1125
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 22.54 %
    Favored  : 73.98 %
  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:  0.93 (0.29), residues: 874
  helix:  2.00 (0.26), residues: 392
  sheet:  0.03 (0.38), residues: 174
  loop : -0.81 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 
 PHE   0.024   0.001   PHE R 165 
 TYR   0.010   0.001   TYR R  90 
 ARG   0.010   0.000   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.659 
Fit side-chains
REVERT: C  251 ASP cc_start: 0.8125 (t0) cc_final: 0.7909 (t0)
REVERT: C  276 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6722 (pm20)
REVERT: D   46 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7316 (mmm-85)
REVERT: D  263 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8435 (m)
REVERT: D  270 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7665 (pp)
REVERT: R  103 LYS cc_start: 0.6706 (ttmm) cc_final: 0.6451 (mmtm)
REVERT: R  192 ASN cc_start: 0.6884 (m-40) cc_final: 0.6495 (t0)
REVERT: R  288 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6443 (pt)
  outliers start: 23
  outliers final: 13
  residues processed: 117
  average time/residue: 1.0288
  time to fit residues: 128.0065
Evaluate side-chains
  115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  164 GLN
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0980
   chunk 82 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 164 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.180418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.137671 restraints weight = 6955.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.95
r_work: 0.3521 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6810  Z= 0.210
  Angle     :  0.569  11.236   9312  Z= 0.295
  Chirality :  0.040   0.130   1127
  Planarity :  0.003   0.044   1155
  Dihedral  :  4.526  54.750   1125
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.30 %
    Favored  : 73.07 %
  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: 874
  helix:  2.03 (0.26), residues: 388
  sheet:  0.12 (0.38), residues: 178
  loop : -0.78 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 
 PHE   0.033   0.001   PHE R 165 
 TYR   0.024   0.001   TYR R  90 
 ARG   0.010   0.000   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  251 ASP cc_start: 0.8173 (t0) cc_final: 0.7949 (t0)
REVERT: C  276 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6700 (pm20)
REVERT: D   46 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7324 (mmm-85)
REVERT: D  263 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8474 (m)
REVERT: D  270 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7732 (pp)
REVERT: R  164 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.5905 (mp-120)
REVERT: R  288 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6469 (pt)
  outliers start: 24
  outliers final: 15
  residues processed: 117
  average time/residue: 0.9554
  time to fit residues: 119.1126
Evaluate side-chains
  118 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  164 GLN
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0770
   chunk 7 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
C 269 ASN
C 306 GLN
D 237 ASN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 139 ASN
R 144 GLN
R 164 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.179656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.136323 restraints weight = 7027.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.02
r_work: 0.3514 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6810  Z= 0.218
  Angle     :  0.579  11.123   9312  Z= 0.301
  Chirality :  0.040   0.131   1127
  Planarity :  0.003   0.047   1155
  Dihedral  :  4.586  56.909   1125
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.84 %
    Favored  : 73.22 %
  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:  0.87 (0.28), residues: 874
  helix:  1.93 (0.26), residues: 392
  sheet:  0.06 (0.38), residues: 178
  loop : -0.87 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 
 PHE   0.033   0.002   PHE R 165 
 TYR   0.012   0.001   TYR R  90 
 ARG   0.011   0.001   ARG C  32 

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: C  251 ASP cc_start: 0.8182 (t0) cc_final: 0.7958 (t0)
REVERT: C  276 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6689 (pm20)
REVERT: D   46 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7341 (mmm-85)
REVERT: D  263 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8463 (m)
REVERT: D  270 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7809 (pp)
REVERT: R  103 LYS cc_start: 0.6766 (ttmm) cc_final: 0.6460 (mmtm)
REVERT: R  192 ASN cc_start: 0.7004 (m-40) cc_final: 0.6550 (t0)
REVERT: R  286 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8075 (p)
REVERT: R  288 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6528 (pt)
  outliers start: 26
  outliers final: 16
  residues processed: 120
  average time/residue: 0.9490
  time to fit residues: 121.3092
Evaluate side-chains
  120 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  254 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   46 ARG
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   80 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  164 GLN
Chi-restraints excluded: chain R residue  286 CYS
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  288 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D 237 ASN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  72 ASN
R 139 ASN
R 164 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.180513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.137013 restraints weight = 6979.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.05
r_work: 0.3530 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6810  Z= 0.200
  Angle     :  0.576  10.995   9312  Z= 0.298
  Chirality :  0.040   0.131   1127
  Planarity :  0.003   0.046   1155
  Dihedral  :  4.597  58.594   1125
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.45 %
    Favored  : 72.92 %
  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 (0.28), residues: 874
  helix:  1.96 (0.26), residues: 386
  sheet: -0.00 (0.37), residues: 178
  loop : -0.86 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 
 PHE   0.034   0.001   PHE R 165 
 TYR   0.026   0.001   TYR R  90 
 ARG   0.011   0.001   ARG C  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6295.19 seconds
wall clock time: 111 minutes 22.57 seconds (6682.57 seconds total)