Starting phenix.real_space_refine
on Tue Mar  3 15:56:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xbw_33107/03_2026/7xbw_33107.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xbw_33107/03_2026/7xbw_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2026/7xbw_33107.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2026/7xbw_33107.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2026/7xbw_33107.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xbw_33107/03_2026/7xbw_33107.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 2}
          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: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ARG:plan': 9, 'ASP:plan': 2}
          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, 'ARG:plan': 2, 'GLU:plan': 4}
          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: {'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1}
          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: 1.37, per 1000 atoms: 0.21
  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: 0.75
  Conformation dependent library (CDL) restraints added in 248.8 milliseconds
  

  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: 0.22
  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: 1.06

  Time building geometry restraints manager: 0.94 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:             1.130
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.520
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.750
-------------------------------------------------------------------------------
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   6811  Z= 0.245
  Angle     :  0.542   8.631   9314  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 : 6.22
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.000   ARG C  32 
 TYR   0.019   0.001   TYR R  90 
 PHE   0.020   0.001   PHE R 110 
 TRP   0.018   0.001   TRP D  82 
 HIS   0.004   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 6810)
  covalent geometry    : angle       0.54211 ( 9312)
  SS BOND              : bond        0.00231 (    1)
  SS BOND              : angle       1.07031 (    2)
  hydrogen bonds       : bond        0.16427 (  368)
  hydrogen bonds       : angle       5.97308 ( 1065)

*********************** 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  : 0.247 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.5181
  time to fit residues: 64.5373
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  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
D  54 HIS
R 170 GLN
R 223 ASN
R 248 ASN
** R 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.180266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.138154 restraints weight = 6915.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.98
r_work: 0.3460 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   6811  Z= 0.267
  Angle     :  0.651   9.757   9314  Z= 0.342
  Chirality :  0.045   0.164   1127
  Planarity :  0.005   0.061   1155
  Dihedral  :  4.974  52.765   1125
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.07 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.28), residues: 874
  helix:  1.73 (0.26), residues: 392
  sheet:  0.06 (0.38), residues: 187
  loop : -0.58 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  32 
 TYR   0.018   0.002   TYR D  59 
 PHE   0.029   0.003   PHE R 110 
 TRP   0.015   0.002   TRP D  82 
 HIS   0.007   0.002   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 ( 6810)
  covalent geometry    : angle       0.65075 ( 9312)
  SS BOND              : bond        0.00338 (    1)
  SS BOND              : angle       1.96764 (    2)
  hydrogen bonds       : bond        0.04356 (  368)
  hydrogen bonds       : angle       5.05451 ( 1065)

*********************** 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
  131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.220 
Fit side-chains
REVERT: C   43 GLU cc_start: 0.5726 (tp30) cc_final: 0.5510 (tp30)
REVERT: C  309 ASP cc_start: 0.7638 (m-30) cc_final: 0.7392 (m-30)
REVERT: D  237 ASN cc_start: 0.7860 (t0) cc_final: 0.7641 (t0)
REVERT: R  288 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6460 (pt)
  outliers start: 16
  outliers final: 6
  residues processed: 124
  average time/residue: 0.4566
  time to fit residues: 60.1558
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  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 37 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
C 188 HIS
D  91 HIS
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 306 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.180594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.131345 restraints weight = 6792.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.15
r_work: 0.3467 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6811  Z= 0.171
  Angle     :  0.561  11.246   9314  Z= 0.290
  Chirality :  0.041   0.139   1127
  Planarity :  0.004   0.055   1155
  Dihedral  :  4.891  55.878   1125
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.31 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.28), residues: 874
  helix:  1.74 (0.26), residues: 391
  sheet: -0.09 (0.39), residues: 175
  loop : -0.72 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 313 
 TYR   0.019   0.001   TYR R  90 
 PHE   0.022   0.002   PHE R 165 
 TRP   0.016   0.002   TRP D  82 
 HIS   0.009   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6810)
  covalent geometry    : angle       0.56069 ( 9312)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       1.80206 (    2)
  hydrogen bonds       : bond        0.03662 (  368)
  hydrogen bonds       : angle       4.76274 ( 1065)

*********************** 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: 24
    poor density    : 107
  time to evaluate  : 0.243 
Fit side-chains
REVERT: C  281 SER cc_start: 0.8130 (t) cc_final: 0.7909 (t)
REVERT: D   45 MET cc_start: 0.5868 (mmt) cc_final: 0.5373 (mmt)
REVERT: D  212 ASP cc_start: 0.8014 (t0) cc_final: 0.7759 (t0)
REVERT: D  270 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7640 (pp)
REVERT: D  304 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7751 (ttm170)
REVERT: R  288 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6535 (pt)
  outliers start: 24
  outliers final: 9
  residues processed: 122
  average time/residue: 0.5063
  time to fit residues: 65.3883
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 ASP
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 D residue  270 ILE
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  238 ILE
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 67 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 285 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 = 0.4116 r_free = 0.4116 target = 0.178360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.133590 restraints weight = 7027.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.22
r_work: 0.3480 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6811  Z= 0.160
  Angle     :  0.560   9.943   9314  Z= 0.289
  Chirality :  0.041   0.137   1127
  Planarity :  0.003   0.050   1155
  Dihedral  :  4.668  54.034   1125
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 18.15 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.28), residues: 874
  helix:  1.79 (0.26), residues: 391
  sheet: -0.22 (0.38), residues: 180
  loop : -0.65 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  32 
 TYR   0.020   0.001   TYR R  90 
 PHE   0.022   0.002   PHE R 165 
 TRP   0.016   0.001   TRP D  82 
 HIS   0.009   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6810)
  covalent geometry    : angle       0.55953 ( 9312)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       1.86856 (    2)
  hydrogen bonds       : bond        0.03479 (  368)
  hydrogen bonds       : angle       4.64909 ( 1065)

*********************** 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
  144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.270 
Fit side-chains
REVERT: D   46 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7262 (mmm160)
REVERT: D  270 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7712 (pp)
REVERT: R  288 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6582 (pt)
  outliers start: 31
  outliers final: 18
  residues processed: 131
  average time/residue: 0.4768
  time to fit residues: 66.2065
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  : 0.245 
-------------------------------------------------------------------------------
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   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   83 THR
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  148 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 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 = 0.178375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.135392 restraints weight = 7080.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.00
r_work: 0.3390 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6811  Z= 0.153
  Angle     :  0.563  12.003   9314  Z= 0.290
  Chirality :  0.041   0.134   1127
  Planarity :  0.003   0.047   1155
  Dihedral  :  4.589  48.542   1125
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.52 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.28), residues: 874
  helix:  1.85 (0.26), residues: 391
  sheet:  0.01 (0.38), residues: 178
  loop : -0.87 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  32 
 TYR   0.021   0.001   TYR R  90 
 PHE   0.020   0.002   PHE R 165 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6810)
  covalent geometry    : angle       0.56223 ( 9312)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       1.83191 (    2)
  hydrogen bonds       : bond        0.03387 (  368)
  hydrogen bonds       : angle       4.57204 ( 1065)

*********************** 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
  127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.262 
Fit side-chains
REVERT: C  276 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6699 (pm20)
REVERT: R  288 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6645 (pt)
  outliers start: 27
  outliers final: 18
  residues processed: 116
  average time/residue: 0.4863
  time to fit residues: 59.8122
Evaluate side-chains
  114 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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   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 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  148 THR
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 79 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 285 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 = 0.4121 r_free = 0.4121 target = 0.178920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.136647 restraints weight = 7033.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 2.02
r_work: 0.3470 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6811  Z= 0.142
  Angle     :  0.549  11.175   9314  Z= 0.284
  Chirality :  0.040   0.134   1127
  Planarity :  0.003   0.046   1155
  Dihedral  :  4.520  48.094   1125
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 20.42 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.29), residues: 874
  helix:  1.88 (0.26), residues: 391
  sheet:  0.00 (0.38), residues: 178
  loop : -0.91 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  32 
 TYR   0.021   0.001   TYR R  90 
 PHE   0.027   0.002   PHE R 165 
 TRP   0.016   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6810)
  covalent geometry    : angle       0.54831 ( 9312)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       1.84351 (    2)
  hydrogen bonds       : bond        0.03264 (  368)
  hydrogen bonds       : angle       4.51708 ( 1065)

*********************** 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
  136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.250 
Fit side-chains
REVERT: C  276 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6696 (pm20)
REVERT: D  270 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7754 (pp)
REVERT: R  288 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6500 (pt)
  outliers start: 27
  outliers final: 15
  residues processed: 126
  average time/residue: 0.4750
  time to fit residues: 63.6825
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  : 0.254 
-------------------------------------------------------------------------------
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   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  270 ILE
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  116 SER
Chi-restraints excluded: chain R residue  242 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 56 optimal weight:    0.4980
   chunk 69 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 285 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 = 0.4131 r_free = 0.4131 target = 0.179597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.137348 restraints weight = 6957.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 1.97
r_work: 0.3493 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6811  Z= 0.136
  Angle     :  0.556  10.320   9314  Z= 0.286
  Chirality :  0.040   0.132   1127
  Planarity :  0.003   0.044   1155
  Dihedral  :  4.485  51.712   1125
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.24 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.29), residues: 874
  helix:  1.90 (0.26), residues: 391
  sheet: -0.00 (0.38), residues: 178
  loop : -0.93 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  32 
 TYR   0.022   0.001   TYR R  90 
 PHE   0.017   0.001   PHE R 165 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6810)
  covalent geometry    : angle       0.55575 ( 9312)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       1.76729 (    2)
  hydrogen bonds       : bond        0.03203 (  368)
  hydrogen bonds       : angle       4.44726 ( 1065)

*********************** 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
  129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.243 
Fit side-chains
REVERT: C  251 ASP cc_start: 0.8207 (t0) cc_final: 0.7980 (t0)
REVERT: C  276 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6633 (pm20)
REVERT: D  270 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7873 (pp)
REVERT: R  103 LYS cc_start: 0.6784 (ttmm) cc_final: 0.6528 (mmtm)
REVERT: R  192 ASN cc_start: 0.7120 (m-40) cc_final: 0.6894 (m-40)
REVERT: R  288 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6672 (pt)
  outliers start: 27
  outliers final: 15
  residues processed: 120
  average time/residue: 0.4565
  time to fit residues: 58.3196
Evaluate side-chains
  110 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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   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  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  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 12 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 58 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 285 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 = 0.4066 r_free = 0.4066 target = 0.172896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.128062 restraints weight = 7086.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.26
r_work: 0.3465 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6811  Z= 0.155
  Angle     :  0.585  12.725   9314  Z= 0.300
  Chirality :  0.041   0.136   1127
  Planarity :  0.003   0.043   1155
  Dihedral  :  4.622  55.674   1125
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.69 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.28), residues: 874
  helix:  1.83 (0.26), residues: 391
  sheet: -0.09 (0.38), residues: 178
  loop : -0.89 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  32 
 TYR   0.010   0.001   TYR R  90 
 PHE   0.026   0.002   PHE R 165 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6810)
  covalent geometry    : angle       0.58399 ( 9312)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       1.95078 (    2)
  hydrogen bonds       : bond        0.03304 (  368)
  hydrogen bonds       : angle       4.48423 ( 1065)

*********************** 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: 25
    poor density    : 102
  time to evaluate  : 0.242 
Fit side-chains
REVERT: C  251 ASP cc_start: 0.8263 (t0) cc_final: 0.8048 (t0)
REVERT: C  276 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6618 (pm20)
REVERT: D  269 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6214 (pp)
REVERT: R  165 PHE cc_start: 0.7622 (p90) cc_final: 0.7411 (p90)
REVERT: R  166 MET cc_start: 0.7643 (ptt) cc_final: 0.7247 (ptp)
REVERT: R  192 ASN cc_start: 0.7142 (m-40) cc_final: 0.6870 (m-40)
REVERT: R  288 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6703 (pt)
  outliers start: 25
  outliers final: 17
  residues processed: 118
  average time/residue: 0.4361
  time to fit residues: 54.8062
Evaluate side-chains
  116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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   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  234 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  269 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  242 LEU
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 22 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 285 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 = 0.4087 r_free = 0.4087 target = 0.175190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.131711 restraints weight = 7054.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.17
r_work: 0.3360 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6811  Z= 0.176
  Angle     :  0.611  12.376   9314  Z= 0.315
  Chirality :  0.042   0.137   1127
  Planarity :  0.004   0.044   1155
  Dihedral  :  4.820  59.121   1125
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.69 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.29), residues: 874
  helix:  1.77 (0.26), residues: 391
  sheet: -0.21 (0.37), residues: 183
  loop : -0.92 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  32 
 TYR   0.022   0.001   TYR R  90 
 PHE   0.028   0.002   PHE R 165 
 TRP   0.015   0.002   TRP D  82 
 HIS   0.008   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6810)
  covalent geometry    : angle       0.61062 ( 9312)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       2.04456 (    2)
  hydrogen bonds       : bond        0.03460 (  368)
  hydrogen bonds       : angle       4.58430 ( 1065)

*********************** 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
  123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.238 
Fit side-chains
REVERT: C  276 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6700 (pm20)
REVERT: D  269 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6152 (pp)
REVERT: R  103 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6582 (mmtm)
REVERT: R  165 PHE cc_start: 0.7738 (p90) cc_final: 0.7514 (p90)
REVERT: R  166 MET cc_start: 0.7601 (ptt) cc_final: 0.7216 (ptp)
REVERT: R  288 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6641 (pt)
  outliers start: 26
  outliers final: 17
  residues processed: 115
  average time/residue: 0.4576
  time to fit residues: 56.0976
Evaluate side-chains
  113 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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   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  269 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  242 LEU
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 39 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 58 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 139 ASN
** 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 = 0.4089 r_free = 0.4089 target = 0.175057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.133711 restraints weight = 7085.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.91
r_work: 0.3394 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6811  Z= 0.153
  Angle     :  0.590  12.026   9314  Z= 0.304
  Chirality :  0.041   0.135   1127
  Planarity :  0.004   0.044   1155
  Dihedral  :  4.746  55.968   1125
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.90 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.28), residues: 874
  helix:  1.78 (0.26), residues: 391
  sheet: -0.21 (0.37), residues: 178
  loop : -0.94 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  32 
 TYR   0.013   0.001   TYR R  90 
 PHE   0.033   0.002   PHE R 295 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.008   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6810)
  covalent geometry    : angle       0.58927 ( 9312)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       2.06401 (    2)
  hydrogen bonds       : bond        0.03321 (  368)
  hydrogen bonds       : angle       4.52688 ( 1065)

********************** 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
  122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.253 
Fit side-chains
REVERT: C  276 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6645 (pm20)
REVERT: D  269 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.6144 (pp)
REVERT: R  103 LYS cc_start: 0.6915 (ttmm) cc_final: 0.6621 (mmtm)
REVERT: R  165 PHE cc_start: 0.7701 (p90) cc_final: 0.7493 (p90)
REVERT: R  166 MET cc_start: 0.7605 (ptt) cc_final: 0.7192 (ptp)
REVERT: R  288 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6611 (pt)
  outliers start: 24
  outliers final: 19
  residues processed: 116
  average time/residue: 0.4540
  time to fit residues: 56.2218
Evaluate side-chains
  117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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   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  269 ILE
Chi-restraints excluded: chain D residue  284 LEU
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  200 PHE
Chi-restraints excluded: chain R residue  242 LEU
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 76 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 72 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN
** R  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  72 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 = 0.4096 r_free = 0.4096 target = 0.175742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.134448 restraints weight = 7026.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.91
r_work: 0.3468 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6811  Z= 0.150
  Angle     :  0.592  11.992   9314  Z= 0.305
  Chirality :  0.041   0.135   1127
  Planarity :  0.004   0.045   1155
  Dihedral  :  4.740  55.215   1125
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 24.36 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.28), residues: 874
  helix:  1.78 (0.26), residues: 391
  sheet: -0.20 (0.37), residues: 178
  loop : -0.94 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  32 
 TYR   0.024   0.001   TYR R  90 
 PHE   0.032   0.002   PHE R 295 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.007   0.001   HIS R 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6810)
  covalent geometry    : angle       0.59096 ( 9312)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       2.05444 (    2)
  hydrogen bonds       : bond        0.03316 (  368)
  hydrogen bonds       : angle       4.50000 ( 1065)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3222.47 seconds
wall clock time: 55 minutes 30.50 seconds (3330.50 seconds total)