Starting phenix.real_space_refine
on Wed Feb 12 17:47:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iod_35616/02_2025/8iod_35616.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iod_35616/02_2025/8iod_35616.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iod_35616/02_2025/8iod_35616.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iod_35616/02_2025/8iod_35616.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iod_35616/02_2025/8iod_35616.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iod_35616/02_2025/8iod_35616.cif"
  }
  resolution = 2.59
  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=  -0.001 sd=   0.051
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: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      67      5.16       5
     C    5110      2.51       5
     N    1401      2.21       5
     O    1482      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Residue "L ASP    2": not complete - not flipped  Time to flip 3 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: 8061
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1943
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2567
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 405
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
    Chain: "L"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 74
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 7, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 5}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'4J2:plan-2': 1, 'NLE:plan-1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "N"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 946
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "R"
      Number of atoms: 2124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2124
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 5, 'TRANS': 264}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.82, per 1000 atoms: 0.60
  Number of scatterers: 8061
  At special positions: 0
  Unit cell: (85.68, 93.177, 127.449, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      67     16.00
     O    1482      8.00
     N    1401      7.00
     C    5110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 264 " - pdb=" SG  CYS R 270 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.19
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  4J2 L   4 "
  Number of C-beta restraints generated:  1926

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 11 sheets defined
      40.1% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.658A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 260 through 270
      removed outlier: 3.528A  pdb=" N   LEU A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 279
      removed outlier: 4.081A  pdb=" N   TYR A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 283
      removed outlier: 3.982A  pdb=" N   ALA A 283 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 283'
    Processing helix  chain 'A' and resid 298 through 317
      removed outlier: 3.524A  pdb=" N   PHE A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 358
      removed outlier: 3.744A  pdb=" N   ILE A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.747A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 43
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.574A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.898A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 43
    Processing helix  chain 'R' and resid 44 through 60
      removed outlier: 3.530A  pdb=" N   GLU R  53 " --> pdb=" O   ILE R  49 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE R  55 " --> pdb=" O   LEU R  51 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LEU R  56 " --> pdb=" O   LEU R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 101
    Processing helix  chain 'R' and resid 107 through 146
    Processing helix  chain 'R' and resid 155 through 180
      removed outlier: 4.399A  pdb=" N   ILE R 178 " --> pdb=" O   GLY R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 220
      removed outlier: 3.882A  pdb=" N   PHE R 194 " --> pdb=" O   LEU R 190 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU R 200 " --> pdb=" O   ALA R 196 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG R 218 " --> pdb=" O   THR R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 233 through 247
      removed outlier: 3.637A  pdb=" N   PHE R 247 " --> pdb=" O   LEU R 243 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 252 through 261
    Processing helix  chain 'R' and resid 267 through 275
      removed outlier: 3.583A  pdb=" N   PHE R 273 " --> pdb=" O   TYR R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 296
      removed outlier: 3.990A  pdb=" N   SER R 288 " --> pdb=" O   ILE R 284 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL R 289 " --> pdb=" O   MET R 285 " (cutoff:3.500A)
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 312
      removed outlier: 3.627A  pdb=" N   CYS R 312 " --> pdb=" O   GLU R 308 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189
      removed outlier: 6.226A  pdb=" N   HIS A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   PHE A 199 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.314A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.390A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.089A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.226A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.838A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.763A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.552A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 320
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6
      removed outlier: 3.776A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.904A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    403 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2029
        1.33 -     1.45: 1651
        1.45 -     1.57: 4443
        1.57 -     1.69: 0
        1.69 -     1.82: 99
  Bond restraints: 8222
  Sorted by residual:
  bond pdb=" CG  ASP L   2 "
       pdb=" OD1 ASP L   2 "
    ideal  model  delta    sigma   weight residual
    1.249  1.287 -0.038 1.90e-02 2.77e+03 4.00e+00
  bond pdb=" CA  4J2 L   4 "
       pdb=" C   4J2 L   4 "
    ideal  model  delta    sigma   weight residual
    1.525  1.559 -0.034 2.10e-02 2.27e+03 2.64e+00
  bond pdb=" CG1 ILE R 178 "
       pdb=" CD1 ILE R 178 "
    ideal  model  delta    sigma   weight residual
    1.513  1.451  0.062 3.90e-02 6.57e+02 2.53e+00
  bond pdb=" CG1 ILE R 144 "
       pdb=" CD1 ILE R 144 "
    ideal  model  delta    sigma   weight residual
    1.513  1.451  0.062 3.90e-02 6.57e+02 2.49e+00
  bond pdb=" CB  THR R 143 "
       pdb=" CG2 THR R 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.87e+00
  ... (remaining 8217 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.51: 11121
        7.51 -    15.01: 2
       15.01 -    22.52: 0
       22.52 -    30.02: 0
       30.02 -    37.53: 1
  Bond angle restraints: 11124
  Sorted by residual:
  angle pdb=" CB  ASP L   2 "
        pdb=" CG  ASP L   2 "
        pdb=" OD1 ASP L   2 "
      ideal   model   delta    sigma   weight residual
     118.40   80.87   37.53 2.30e+00 1.89e-01 2.66e+02
  angle pdb=" N   ILE R 178 "
        pdb=" CA  ILE R 178 "
        pdb=" C   ILE R 178 "
      ideal   model   delta    sigma   weight residual
     113.71  109.76    3.95 9.50e-01 1.11e+00 1.73e+01
  angle pdb=" C   ARG N  98 "
        pdb=" N   CYS N  99 "
        pdb=" CA  CYS N  99 "
      ideal   model   delta    sigma   weight residual
     123.65  116.01    7.64 1.88e+00 2.83e-01 1.65e+01
  angle pdb=" N   TRP R 251 "
        pdb=" CA  TRP R 251 "
        pdb=" C   TRP R 251 "
      ideal   model   delta    sigma   weight residual
     110.61  115.59   -4.98 1.25e+00 6.40e-01 1.59e+01
  angle pdb=" C   ILE B  58 "
        pdb=" N   TYR B  59 "
        pdb=" CA  TYR B  59 "
      ideal   model   delta    sigma   weight residual
     122.23  116.01    6.22 1.57e+00 4.06e-01 1.57e+01
  ... (remaining 11119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4398
       17.52 -    35.05: 411
       35.05 -    52.57: 71
       52.57 -    70.09: 11
       70.09 -    87.61: 8
  Dihedral angle restraints: 4899
    sinusoidal: 1923
      harmonic: 2976
  Sorted by residual:
  dihedral pdb=" CH3 ACE L   0 "
           pdb=" C   ACE L   0 "
           pdb=" N   NLE L   1 "
           pdb=" CA  NLE L   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -119.60  -60.40     1      5.00e+00 4.00e-02 1.94e+02
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -8.62  -77.38     1      1.00e+01 1.00e-02 7.50e+01
  dihedral pdb=" CA  TRP R 251 "
           pdb=" C   TRP R 251 "
           pdb=" N   ALA R 252 "
           pdb=" CA  ALA R 252 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.68   34.32     0      5.00e+00 4.00e-02 4.71e+01
  ... (remaining 4896 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 864
       0.042 -    0.084: 295
       0.084 -    0.127: 76
       0.127 -    0.169: 17
       0.169 -    0.211: 4
  Chirality restraints: 1256
  Sorted by residual:
  chirality pdb=" CA  PHE B 292 "
            pdb=" N   PHE B 292 "
            pdb=" C   PHE B 292 "
            pdb=" CB  PHE B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  TRP R 251 "
            pdb=" N   TRP R 251 "
            pdb=" C   TRP R 251 "
            pdb=" CB  TRP R 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.34e-01
  chirality pdb=" CA  ASN A 195 "
            pdb=" N   ASN A 195 "
            pdb=" C   ASN A 195 "
            pdb=" CB  ASN A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.58e-01
  ... (remaining 1253 not shown)

  Planarity restraints: 1411
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ACE L   0 "    0.077 2.00e-02 2.50e+03   2.63e-01 8.68e+02
        pdb=" O   ACE L   0 "   -0.040 2.00e-02 2.50e+03
        pdb=" CH3 ACE L   0 "   -0.183 2.00e-02 2.50e+03
        pdb=" N   NLE L   1 "    0.457 2.00e-02 2.50e+03
        pdb=" CA  NLE L   1 "   -0.312 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 251 "    0.025 2.00e-02 2.50e+03   2.35e-02 1.38e+01
        pdb=" CG  TRP R 251 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 251 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 251 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 251 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 251 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 251 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 251 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 251 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 251 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  59 "    0.052 5.00e-02 4.00e+02   7.94e-02 1.01e+01
        pdb=" N   PRO G  60 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1408 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 96
        2.61 -     3.18: 7171
        3.18 -     3.76: 12962
        3.76 -     4.33: 18198
        4.33 -     4.90: 29533
  Nonbonded interactions: 67960
  Sorted by model distance:
  nonbonded pdb=" CG  ASP L   2 "
            pdb=" NZ  LYS L   7 "
     model   vdw
     2.038 3.350
  nonbonded pdb=" OG  SER B 275 "
            pdb=" O   SER B 316 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   TYR B  85 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.221 3.040
  ... (remaining 67955 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:             1.480
  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:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.660
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
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   0.062   8222  Z= 0.301
  Angle     :  0.798  37.529  11124  Z= 0.444
  Chirality :  0.047   0.211   1256
  Planarity :  0.009   0.263   1411
  Dihedral  : 14.071  87.614   2964
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.83 (0.26), residues: 1001
  helix: -0.08 (0.26), residues: 396
  sheet: -0.53 (0.33), residues: 225
  loop : -0.88 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP R 251 
 HIS   0.017   0.002   HIS B  62 
 PHE   0.024   0.002   PHE B 151 
 TYR   0.011   0.002   TYR A 278 
 ARG   0.006   0.000   ARG N  98 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.835 
Fit side-chains
REVERT: G   21 MET cc_start: 0.5680 (ptp) cc_final: 0.5129 (ptp)
REVERT: G   44 HIS cc_start: 0.6793 (m-70) cc_final: 0.6557 (t-90)
  outliers start: 0
  outliers final: 1
  residues processed: 115
  average time/residue: 1.0599
  time to fit residues: 130.7261
Evaluate side-chains
  93 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 231 ASN
** A 354 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 = 0.4651 r_free = 0.4651 target = 0.219482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.178445 restraints weight = 7411.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.4285 rms_B_bonded: 2.64
r_work: 0.3867 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8222  Z= 0.231
  Angle     :  0.591   6.880  11124  Z= 0.318
  Chirality :  0.043   0.154   1256
  Planarity :  0.005   0.070   1411
  Dihedral  :  5.204  37.498   1122
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  8.01 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.27), residues: 1001
  helix:  0.66 (0.26), residues: 394
  sheet: -0.34 (0.33), residues: 228
  loop : -0.64 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP R 251 
 HIS   0.011   0.001   HIS A 324 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.010   0.001   TYR R  72 
 ARG   0.005   0.000   ARG A 209 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A  256 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6683 (mp)
REVERT: B  220 GLN cc_start: 0.6987 (mp10) cc_final: 0.6706 (mp10)
REVERT: B  269 ILE cc_start: 0.7805 (pt) cc_final: 0.7055 (tp)
REVERT: G   21 MET cc_start: 0.5164 (ptp) cc_final: 0.4748 (ptp)
REVERT: G   44 HIS cc_start: 0.6771 (m-70) cc_final: 0.6127 (t-90)
REVERT: R   83 MET cc_start: 0.6579 (tpp) cc_final: 0.5828 (ttp)
REVERT: R  235 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6897 (tp-100)
  outliers start: 20
  outliers final: 8
  residues processed: 110
  average time/residue: 1.0680
  time to fit residues: 126.5683
Evaluate side-chains
  104 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  106 ILE
Chi-restraints excluded: chain R residue  235 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 65 optimal weight:    0.4980
   chunk 88 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
A 246 ASN
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.221633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.179059 restraints weight = 7532.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 2.44
r_work: 0.3938 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8222  Z= 0.175
  Angle     :  0.528   5.821  11124  Z= 0.285
  Chirality :  0.041   0.142   1256
  Planarity :  0.004   0.065   1411
  Dihedral  :  4.945  53.236   1122
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 10.76 %
    Favored  : 86.84 %
  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:  0.16 (0.27), residues: 1001
  helix:  1.11 (0.27), residues: 394
  sheet: -0.27 (0.33), residues: 226
  loop : -0.59 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 251 
 HIS   0.007   0.001   HIS A 324 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.010   0.001   TYR R  72 
 ARG   0.004   0.000   ARG R 140 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.927 
Fit side-chains
REVERT: B  220 GLN cc_start: 0.6900 (mp10) cc_final: 0.6532 (mp10)
REVERT: G   21 MET cc_start: 0.5455 (ptp) cc_final: 0.4819 (mtt)
REVERT: G   44 HIS cc_start: 0.6762 (m-70) cc_final: 0.6236 (t-170)
REVERT: R   83 MET cc_start: 0.6646 (tpp) cc_final: 0.5931 (ttp)
REVERT: R  178 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5898 (mt)
REVERT: R  297 PHE cc_start: 0.6479 (m-80) cc_final: 0.6132 (m-80)
  outliers start: 21
  outliers final: 9
  residues processed: 111
  average time/residue: 1.0564
  time to fit residues: 126.0751
Evaluate side-chains
  100 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue  106 ILE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 31 optimal weight:    0.3980
   chunk 75 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
A 246 ASN
** A 354 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 = 0.4656 r_free = 0.4656 target = 0.220358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.176202 restraints weight = 7456.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.4341 rms_B_bonded: 3.15
r_work: 0.4079 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3954 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8222  Z= 0.197
  Angle     :  0.531   5.752  11124  Z= 0.286
  Chirality :  0.042   0.145   1256
  Planarity :  0.004   0.060   1411
  Dihedral  :  4.608  24.845   1120
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.04 %
    Favored  : 84.10 %
  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:  0.19 (0.27), residues: 1001
  helix:  1.23 (0.27), residues: 392
  sheet: -0.37 (0.33), residues: 228
  loop : -0.60 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 251 
 HIS   0.007   0.001   HIS A 324 
 PHE   0.014   0.002   PHE B 151 
 TYR   0.010   0.001   TYR R  72 
 ARG   0.002   0.000   ARG R 298 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.6824 (ttp) cc_final: 0.6621 (ttp)
REVERT: B   96 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7483 (mmp-170)
REVERT: B  220 GLN cc_start: 0.6914 (mp10) cc_final: 0.5842 (tm-30)
REVERT: G   21 MET cc_start: 0.5639 (ptp) cc_final: 0.4730 (mtt)
REVERT: G   44 HIS cc_start: 0.6732 (m-70) cc_final: 0.6243 (t-170)
REVERT: N  117 TYR cc_start: 0.5336 (OUTLIER) cc_final: 0.3738 (p90)
REVERT: R   83 MET cc_start: 0.6782 (tpp) cc_final: 0.6056 (ttp)
REVERT: R  178 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.5883 (mt)
REVERT: R  285 MET cc_start: 0.7471 (ttm) cc_final: 0.7222 (mtp)
REVERT: R  297 PHE cc_start: 0.6523 (m-80) cc_final: 0.6200 (m-80)
  outliers start: 25
  outliers final: 11
  residues processed: 108
  average time/residue: 1.0576
  time to fit residues: 122.9923
Evaluate side-chains
  106 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  106 ILE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  284 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    0.0040
   chunk 92 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 72 optimal weight:    7.9990
   chunk 8 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.8796

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
** A 354 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 = 0.4646 r_free = 0.4646 target = 0.219074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.167175 restraints weight = 7377.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 1.98
r_work: 0.3920 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3776 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8222  Z= 0.222
  Angle     :  0.544   5.771  11124  Z= 0.292
  Chirality :  0.042   0.144   1256
  Planarity :  0.004   0.057   1411
  Dihedral  :  4.651  26.208   1120
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.22 %
    Favored  : 81.46 %
  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:  0.14 (0.27), residues: 1001
  helix:  1.18 (0.26), residues: 392
  sheet: -0.43 (0.33), residues: 230
  loop : -0.59 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 251 
 HIS   0.007   0.001   HIS A 324 
 PHE   0.017   0.002   PHE B 151 
 TYR   0.011   0.001   TYR R  72 
 ARG   0.003   0.000   ARG A  15 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5391 (mm-30)
REVERT: B   96 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7640 (mmp-170)
REVERT: B  220 GLN cc_start: 0.6875 (mp10) cc_final: 0.5799 (tm-30)
REVERT: G   21 MET cc_start: 0.5450 (ptp) cc_final: 0.4764 (mtt)
REVERT: G   44 HIS cc_start: 0.6763 (m-70) cc_final: 0.6158 (t-170)
REVERT: N  117 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.3567 (p90)
REVERT: R   43 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.5335 (t80)
REVERT: R   83 MET cc_start: 0.6831 (tpp) cc_final: 0.6017 (ttp)
REVERT: R  178 ILE cc_start: 0.6420 (OUTLIER) cc_final: 0.5921 (mt)
REVERT: R  235 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6907 (tp-100)
REVERT: R  285 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7175 (mtp)
REVERT: R  297 PHE cc_start: 0.6525 (m-80) cc_final: 0.6160 (m-80)
  outliers start: 29
  outliers final: 13
  residues processed: 110
  average time/residue: 1.0492
  time to fit residues: 124.0214
Evaluate side-chains
  108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  106 ILE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  235 GLN
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  282 ILE
Chi-restraints excluded: chain R residue  284 ILE
Chi-restraints excluded: chain R residue  285 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 25 optimal weight:   30.0000
   chunk 54 optimal weight:    0.0970
   chunk 65 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 44 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
** A 354 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 = 0.4643 r_free = 0.4643 target = 0.218634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.174014 restraints weight = 7421.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.4218 rms_B_bonded: 2.73
r_work: 0.3874 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6583
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8222  Z= 0.240
  Angle     :  0.555   5.960  11124  Z= 0.298
  Chirality :  0.043   0.143   1256
  Planarity :  0.004   0.053   1411
  Dihedral  :  4.685  24.833   1120
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.48 %
    Favored  : 79.98 %
  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:  0.10 (0.27), residues: 1001
  helix:  1.12 (0.26), residues: 394
  sheet: -0.46 (0.33), residues: 230
  loop : -0.59 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 251 
 HIS   0.008   0.001   HIS A 324 
 PHE   0.018   0.002   PHE A 199 
 TYR   0.012   0.001   TYR R  72 
 ARG   0.006   0.000   ARG A 209 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5273 (mm-30)
REVERT: B   96 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7584 (mmp-170)
REVERT: B  220 GLN cc_start: 0.6850 (mp10) cc_final: 0.5811 (tm-30)
REVERT: G   21 MET cc_start: 0.5265 (ptp) cc_final: 0.4807 (mtt)
REVERT: G   44 HIS cc_start: 0.6979 (m-70) cc_final: 0.6175 (t-170)
REVERT: N  117 TYR cc_start: 0.5198 (OUTLIER) cc_final: 0.3121 (p90)
REVERT: R   43 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5546 (t80)
REVERT: R   83 MET cc_start: 0.6732 (tpp) cc_final: 0.5927 (ttp)
REVERT: R  178 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.6025 (mt)
REVERT: R  187 ILE cc_start: 0.5890 (OUTLIER) cc_final: 0.5582 (mm)
REVERT: R  235 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6763 (tp-100)
REVERT: R  285 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7083 (mtp)
REVERT: R  297 PHE cc_start: 0.6526 (m-80) cc_final: 0.6187 (m-80)
  outliers start: 31
  outliers final: 15
  residues processed: 107
  average time/residue: 1.0338
  time to fit residues: 119.1287
Evaluate side-chains
  112 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  235 GLN
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  282 ILE
Chi-restraints excluded: chain R residue  284 ILE
Chi-restraints excluded: chain R residue  285 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0020
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
** A 354 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 = 0.4663 r_free = 0.4663 target = 0.220987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.178975 restraints weight = 7408.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.4292 rms_B_bonded: 2.37
r_work: 0.3926 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8222  Z= 0.177
  Angle     :  0.516   6.401  11124  Z= 0.279
  Chirality :  0.041   0.152   1256
  Planarity :  0.004   0.050   1411
  Dihedral  :  4.481  23.107   1120
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.93 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.27), residues: 1001
  helix:  1.35 (0.27), residues: 394
  sheet: -0.36 (0.33), residues: 227
  loop : -0.55 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 251 
 HIS   0.006   0.001   HIS A 324 
 PHE   0.018   0.001   PHE A 199 
 TYR   0.012   0.001   TYR R  72 
 ARG   0.004   0.000   ARG A 209 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.4957 (mm-30)
REVERT: B   96 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7582 (mmp-170)
REVERT: B  218 CYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7257 (t)
REVERT: B  220 GLN cc_start: 0.6804 (mp10) cc_final: 0.5710 (tm-30)
REVERT: B  222 PHE cc_start: 0.5784 (m-80) cc_final: 0.5579 (m-80)
REVERT: G   21 MET cc_start: 0.5091 (ptp) cc_final: 0.4453 (mtt)
REVERT: G   44 HIS cc_start: 0.6938 (m-70) cc_final: 0.6201 (t-170)
REVERT: N  117 TYR cc_start: 0.5230 (OUTLIER) cc_final: 0.3125 (p90)
REVERT: R   43 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5483 (t80)
REVERT: R   83 MET cc_start: 0.6731 (tpp) cc_final: 0.5964 (ttp)
REVERT: R  178 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5808 (mt)
REVERT: R  235 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6800 (tp-100)
REVERT: R  285 MET cc_start: 0.7388 (ttm) cc_final: 0.7054 (mtp)
REVERT: R  290 MET cc_start: 0.6268 (tpp) cc_final: 0.5820 (mmm)
REVERT: R  297 PHE cc_start: 0.6528 (m-80) cc_final: 0.6193 (m-80)
  outliers start: 29
  outliers final: 17
  residues processed: 112
  average time/residue: 0.9870
  time to fit residues: 119.2628
Evaluate side-chains
  112 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  235 GLN
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  282 ILE
Chi-restraints excluded: chain R residue  284 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:   30.0000
   chunk 45 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 26 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 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 = 0.4596 r_free = 0.4596 target = 0.213065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.160562 restraints weight = 7580.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 2.03
r_work: 0.3818 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6831
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.094   8222  Z= 0.492
  Angle     :  0.733   7.979  11124  Z= 0.392
  Chirality :  0.050   0.214   1256
  Planarity :  0.006   0.058   1411
  Dihedral  :  5.305  27.903   1120
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.73 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.43 (0.26), residues: 1001
  helix:  0.42 (0.26), residues: 393
  sheet: -0.50 (0.33), residues: 233
  loop : -0.73 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B  99 
 HIS   0.008   0.002   HIS A 324 
 PHE   0.036   0.003   PHE B 151 
 TYR   0.020   0.003   TYR R  72 
 ARG   0.007   0.001   ARG A 209 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A  235 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5749 (mm-30)
REVERT: B  214 ARG cc_start: 0.6224 (mmp-170) cc_final: 0.5931 (mmp-170)
REVERT: B  220 GLN cc_start: 0.7100 (mp10) cc_final: 0.6808 (mp10)
REVERT: G   21 MET cc_start: 0.4901 (ptp) cc_final: 0.4332 (mtt)
REVERT: N   98 ARG cc_start: 0.6926 (ttp-170) cc_final: 0.6437 (ttm170)
REVERT: N  117 TYR cc_start: 0.5982 (OUTLIER) cc_final: 0.3499 (p90)
REVERT: R   43 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5669 (t80)
REVERT: R   64 ASN cc_start: 0.6169 (t0) cc_final: 0.5841 (t0)
REVERT: R  178 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6420 (mt)
REVERT: R  187 ILE cc_start: 0.5851 (OUTLIER) cc_final: 0.5604 (mm)
REVERT: R  235 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6446 (tt0)
REVERT: R  290 MET cc_start: 0.6582 (tpp) cc_final: 0.6236 (mmm)
REVERT: R  297 PHE cc_start: 0.6571 (m-80) cc_final: 0.6267 (m-80)
  outliers start: 28
  outliers final: 12
  residues processed: 112
  average time/residue: 1.0545
  time to fit residues: 126.7062
Evaluate side-chains
  111 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  235 GLN
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  282 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
A 246 ASN
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.218497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.175166 restraints weight = 7567.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4230 rms_B_bonded: 2.65
r_work: 0.3898 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8222  Z= 0.220
  Angle     :  0.590  11.264  11124  Z= 0.314
  Chirality :  0.043   0.161   1256
  Planarity :  0.004   0.054   1411
  Dihedral  :  4.990  36.410   1120
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.96 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -0.01 (0.27), residues: 1001
  helix:  0.98 (0.26), residues: 394
  sheet: -0.41 (0.34), residues: 228
  loop : -0.66 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 251 
 HIS   0.007   0.001   HIS A 324 
 PHE   0.025   0.002   PHE A 199 
 TYR   0.013   0.001   TYR N  60 
 ARG   0.006   0.000   ARG A 209 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  235 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.5019 (mm-30)
REVERT: B   96 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7581 (mmp-170)
REVERT: B  198 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.5893 (pp)
REVERT: B  214 ARG cc_start: 0.6205 (mmp-170) cc_final: 0.6002 (mmp-170)
REVERT: B  218 CYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7302 (t)
REVERT: B  220 GLN cc_start: 0.6899 (mp10) cc_final: 0.5925 (tm-30)
REVERT: G   21 MET cc_start: 0.5208 (ptp) cc_final: 0.4546 (mtt)
REVERT: G   44 HIS cc_start: 0.6818 (m-70) cc_final: 0.6252 (t-170)
REVERT: N  117 TYR cc_start: 0.5524 (OUTLIER) cc_final: 0.3512 (p90)
REVERT: R   43 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5364 (t80)
REVERT: R   83 MET cc_start: 0.6529 (tpp) cc_final: 0.5704 (ttp)
REVERT: R  178 ILE cc_start: 0.6339 (OUTLIER) cc_final: 0.5966 (mt)
REVERT: R  187 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5626 (mm)
REVERT: R  235 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6806 (tp-100)
REVERT: R  285 MET cc_start: 0.7437 (ttm) cc_final: 0.7119 (mtp)
REVERT: R  297 PHE cc_start: 0.6501 (m-80) cc_final: 0.6195 (m-80)
  outliers start: 27
  outliers final: 10
  residues processed: 111
  average time/residue: 0.9732
  time to fit residues: 116.5135
Evaluate side-chains
  108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  235 GLN
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  282 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0970
   chunk 78 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 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 = 0.4668 r_free = 0.4668 target = 0.221720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.176972 restraints weight = 7436.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.4362 rms_B_bonded: 2.76
r_work: 0.4120 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3994 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6636
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8222  Z= 0.175
  Angle     :  0.554  10.297  11124  Z= 0.295
  Chirality :  0.042   0.154   1256
  Planarity :  0.004   0.052   1411
  Dihedral  :  4.707  34.326   1120
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.11 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  0.29 (0.27), residues: 1001
  helix:  1.35 (0.27), residues: 394
  sheet: -0.37 (0.34), residues: 227
  loop : -0.57 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 251 
 HIS   0.005   0.001   HIS A 324 
 PHE   0.019   0.001   PHE A 199 
 TYR   0.014   0.001   TYR N  60 
 ARG   0.005   0.000   ARG A 209 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  231 ASN cc_start: 0.7435 (t0) cc_final: 0.7201 (m-40)
REVERT: A  235 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.5100 (mm-30)
REVERT: B   96 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7650 (mmp-170)
REVERT: B  198 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6130 (pp)
REVERT: B  217 MET cc_start: 0.7263 (mtt) cc_final: 0.7002 (mmt)
REVERT: B  218 CYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6987 (t)
REVERT: B  220 GLN cc_start: 0.6978 (mp10) cc_final: 0.6699 (mp10)
REVERT: G   21 MET cc_start: 0.5372 (ptp) cc_final: 0.4610 (mtt)
REVERT: G   44 HIS cc_start: 0.6952 (m-70) cc_final: 0.6143 (t-170)
REVERT: N  117 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.3422 (p90)
REVERT: R   43 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5453 (t80)
REVERT: R   83 MET cc_start: 0.6704 (tpp) cc_final: 0.5908 (ttp)
REVERT: R  178 ILE cc_start: 0.6194 (OUTLIER) cc_final: 0.5675 (mt)
REVERT: R  285 MET cc_start: 0.7398 (ttm) cc_final: 0.7154 (mtp)
REVERT: R  290 MET cc_start: 0.6384 (tpp) cc_final: 0.5982 (mmm)
REVERT: R  297 PHE cc_start: 0.6523 (m-80) cc_final: 0.6219 (m-80)
  outliers start: 20
  outliers final: 9
  residues processed: 106
  average time/residue: 0.9681
  time to fit residues: 110.6589
Evaluate side-chains
  100 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   42 VAL
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  262 LEU
Chi-restraints excluded: chain R residue  282 ILE
Chi-restraints excluded: chain R residue  284 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0000
   chunk 23 optimal weight:    0.0670
   chunk 50 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0970
   chunk 43 optimal weight:    0.4980
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.2520

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 245 ASN
A 246 ASN
A 338 ASN
A 354 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.225258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.181744 restraints weight = 7509.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.4321 rms_B_bonded: 2.37
r_work: 0.3987 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6490
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8222  Z= 0.146
  Angle     :  0.526   9.792  11124  Z= 0.280
  Chirality :  0.041   0.153   1256
  Planarity :  0.004   0.050   1411
  Dihedral  :  4.465  31.915   1120
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.79 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  0.47 (0.27), residues: 1001
  helix:  1.54 (0.27), residues: 397
  sheet: -0.26 (0.34), residues: 220
  loop : -0.56 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 251 
 HIS   0.004   0.001   HIS A 324 
 PHE   0.013   0.001   PHE A 199 
 TYR   0.015   0.001   TYR N  60 
 ARG   0.004   0.000   ARG A 209 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11904.04 seconds
wall clock time: 209 minutes 30.99 seconds (12570.99 seconds total)