Starting phenix.real_space_refine
on Wed Mar 12 18:32:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iod_35616/03_2025/8iod_35616.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iod_35616/03_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_35616/03_2025/8iod_35616.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iod_35616/03_2025/8iod_35616.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iod_35616/03_2025/8iod_35616.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iod_35616/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.64, per 1000 atoms: 0.70
  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: 2.43
  Conformation dependent library (CDL) restraints added in 918.0 milliseconds
  

  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: 0.97
  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: 3.22

  Time building geometry restraints manager: 2.84 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:             1.410
  Set stop_for_unknowns flag:              0.010
  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:          0.430
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.780
  Find NCS groups from input model:        0.090
  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:17.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.060
-------------------------------------------------------------------------------
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  : 0.903 
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: 1.0369
  time to fit residues: 127.9331
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  : 0.820 
-------------------------------------------------------------------------------
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 = 0.178446 restraints weight = 7411.297|
|-----------------------------------------------------------------------------|
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: 0.6624
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  37.499   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  : 0.888 
Fit side-chains
REVERT: A  256 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6681 (mp)
REVERT: B  220 GLN cc_start: 0.6986 (mp10) cc_final: 0.6704 (mp10)
REVERT: B  269 ILE cc_start: 0.7805 (pt) cc_final: 0.7056 (tp)
REVERT: G   21 MET cc_start: 0.5155 (ptp) cc_final: 0.4740 (ptp)
REVERT: G   44 HIS cc_start: 0.6771 (m-70) cc_final: 0.6119 (t-90)
REVERT: R   83 MET cc_start: 0.6578 (tpp) cc_final: 0.5827 (ttp)
REVERT: R  235 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6895 (tp-100)
  outliers start: 20
  outliers final: 8
  residues processed: 110
  average time/residue: 0.9955
  time to fit residues: 118.0356
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  : 0.871 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 88 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0970
   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
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 = 0.4673 r_free = 0.4673 target = 0.222102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.178446 restraints weight = 7541.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.4261 rms_B_bonded: 2.99
r_work: 0.3950 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.1479

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= 0.170
  Angle     :  0.523   5.813  11124  Z= 0.283
  Chirality :  0.041   0.142   1256
  Planarity :  0.004   0.065   1411
  Dihedral  :  4.905  52.530   1122
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 10.64 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.27), residues: 1001
  helix:  1.13 (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   0.026   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   0.003   0.000   ARG A 209 

*********************** 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
  120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.969 
Fit side-chains
REVERT: B  220 GLN cc_start: 0.6879 (mp10) cc_final: 0.6503 (mp10)
REVERT: G   21 MET cc_start: 0.5494 (ptp) cc_final: 0.4859 (mtt)
REVERT: G   44 HIS cc_start: 0.6745 (m-70) cc_final: 0.6253 (t-170)
REVERT: R   83 MET cc_start: 0.6626 (tpp) cc_final: 0.5898 (ttp)
REVERT: R  178 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5832 (mt)
REVERT: R  297 PHE cc_start: 0.6469 (m-80) cc_final: 0.6117 (m-80)
  outliers start: 20
  outliers final: 8
  residues processed: 111
  average time/residue: 1.1053
  time to fit residues: 132.2308
Evaluate side-chains
  100 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
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 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:    5.9990
   chunk 79 optimal weight:    0.2980
   chunk 91 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 61 optimal weight:   10.0000
   chunk 31 optimal weight:    0.3980
   chunk 75 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4667 r_free = 0.4667 target = 0.221477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.177474 restraints weight = 7461.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.4248 rms_B_bonded: 2.59
r_work: 0.3921 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6513
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8222  Z= 0.179
  Angle     :  0.518   5.731  11124  Z= 0.279
  Chirality :  0.041   0.144   1256
  Planarity :  0.004   0.058   1411
  Dihedral  :  4.530  24.143   1120
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.16 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.27), residues: 1001
  helix:  1.31 (0.27), residues: 392
  sheet: -0.33 (0.33), residues: 227
  loop : -0.61 (0.32), residues: 382

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   0.013   0.001   PHE B 151 
 TYR   0.009   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
  120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 ARG cc_start: 0.7900 (mtp180) cc_final: 0.7385 (mmp-170)
REVERT: B  220 GLN cc_start: 0.6812 (mp10) cc_final: 0.5517 (tm-30)
REVERT: B  222 PHE cc_start: 0.5862 (m-80) cc_final: 0.5537 (m-80)
REVERT: G   21 MET cc_start: 0.5576 (ptp) cc_final: 0.4789 (mtt)
REVERT: G   44 HIS cc_start: 0.6916 (m-70) cc_final: 0.6160 (t-170)
REVERT: N  117 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.3559 (p90)
REVERT: R   83 MET cc_start: 0.6676 (tpp) cc_final: 0.5913 (ttp)
REVERT: R  178 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5866 (mt)
REVERT: R  285 MET cc_start: 0.7383 (ttm) cc_final: 0.7148 (mtp)
REVERT: R  297 PHE cc_start: 0.6486 (m-80) cc_final: 0.6156 (m-80)
  outliers start: 23
  outliers final: 11
  residues processed: 110
  average time/residue: 1.1573
  time to fit residues: 136.9668
Evaluate side-chains
  107 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0060
   chunk 55 optimal weight:    0.0060
   chunk 4 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5412

-------------------------------------------------------------------------------
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 = 0.4666 r_free = 0.4666 target = 0.221708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.177185 restraints weight = 7364.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.4248 rms_B_bonded: 2.57
r_work: 0.3928 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.1845

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= 0.170
  Angle     :  0.506   5.731  11124  Z= 0.272
  Chirality :  0.041   0.144   1256
  Planarity :  0.004   0.054   1411
  Dihedral  :  4.450  24.564   1120
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.33 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.27), residues: 1001
  helix:  1.41 (0.27), residues: 392
  sheet: -0.34 (0.33), residues: 227
  loop : -0.57 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 251 
 HIS   0.006   0.001   HIS A 324 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.009   0.001   TYR R  72 
 ARG   0.005   0.000   ARG A 209 

*********************** 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: 24
    poor density    : 98
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5214 (mm-30)
REVERT: A  353 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6819 (tmm)
REVERT: B   96 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7484 (mmp-170)
REVERT: B  220 GLN cc_start: 0.6871 (mp10) cc_final: 0.5559 (tm-30)
REVERT: B  222 PHE cc_start: 0.5966 (m-80) cc_final: 0.5656 (m-80)
REVERT: G   21 MET cc_start: 0.5458 (ptp) cc_final: 0.4801 (mtt)
REVERT: G   44 HIS cc_start: 0.6902 (m-70) cc_final: 0.6185 (t-170)
REVERT: N  117 TYR cc_start: 0.5327 (OUTLIER) cc_final: 0.3433 (p90)
REVERT: R   43 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.5356 (t80)
REVERT: R   83 MET cc_start: 0.6717 (tpp) cc_final: 0.5938 (ttp)
REVERT: R  178 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5811 (mt)
REVERT: R  285 MET cc_start: 0.7389 (ttm) cc_final: 0.7092 (mtp)
REVERT: R  297 PHE cc_start: 0.6485 (m-80) cc_final: 0.6156 (m-80)
  outliers start: 24
  outliers final: 10
  residues processed: 111
  average time/residue: 1.0134
  time to fit residues: 120.8627
Evaluate side-chains
  106 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  353 MET
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   43 PHE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 25 optimal weight:   30.0000
   chunk 54 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4642 r_free = 0.4642 target = 0.218715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.163157 restraints weight = 7413.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.4107 rms_B_bonded: 2.20
r_work: 0.3895 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8222  Z= 0.259
  Angle     :  0.566   6.104  11124  Z= 0.304
  Chirality :  0.043   0.161   1256
  Planarity :  0.004   0.053   1411
  Dihedral  :  4.685  24.906   1120
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.59 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.27), residues: 1001
  helix:  1.20 (0.26), residues: 392
  sheet: -0.39 (0.33), residues: 229
  loop : -0.59 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 251 
 HIS   0.008   0.001   HIS A 324 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.012   0.002   TYR R  72 
 ARG   0.004   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: 26
    poor density    : 97
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5348 (mm-30)
REVERT: B   96 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7579 (mmp-170)
REVERT: B  220 GLN cc_start: 0.6969 (mp10) cc_final: 0.5868 (tm-30)
REVERT: G   21 MET cc_start: 0.5176 (ptp) cc_final: 0.4744 (mtt)
REVERT: G   44 HIS cc_start: 0.6971 (m-70) cc_final: 0.6102 (t-170)
REVERT: N  117 TYR cc_start: 0.5264 (OUTLIER) cc_final: 0.3083 (p90)
REVERT: R   43 PHE cc_start: 0.6229 (OUTLIER) cc_final: 0.5447 (t80)
REVERT: R   83 MET cc_start: 0.6878 (tpp) cc_final: 0.6095 (ttp)
REVERT: R  178 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6058 (mt)
REVERT: R  235 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6914 (tp-100)
REVERT: R  285 MET cc_start: 0.7505 (ttm) cc_final: 0.7180 (mtp)
REVERT: R  297 PHE cc_start: 0.6449 (m-80) cc_final: 0.6141 (m-80)
  outliers start: 26
  outliers final: 14
  residues processed: 111
  average time/residue: 1.0637
  time to fit residues: 128.1755
Evaluate side-chains
  110 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 87 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 95 optimal weight:    8.9990
   chunk 94 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4645 r_free = 0.4645 target = 0.218722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.162528 restraints weight = 7434.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.4099 rms_B_bonded: 1.94
r_work: 0.3912 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
moved from start:          0.1814

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= 0.247
  Angle     :  0.562   6.419  11124  Z= 0.303
  Chirality :  0.043   0.174   1256
  Planarity :  0.004   0.051   1411
  Dihedral  :  4.700  24.570   1120
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 17.16 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.14 (0.26), residues: 394
  sheet: -0.38 (0.34), residues: 230
  loop : -0.54 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 251 
 HIS   0.007   0.001   HIS A 324 
 PHE   0.021   0.002   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
  120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  235 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5328 (mm-30)
REVERT: B   96 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7609 (mmp-170)
REVERT: B  220 GLN cc_start: 0.6959 (mp10) cc_final: 0.5845 (tm-30)
REVERT: G   21 MET cc_start: 0.5061 (ptp) cc_final: 0.4486 (mtt)
REVERT: G   44 HIS cc_start: 0.6980 (m-70) cc_final: 0.6094 (t-170)
REVERT: N  117 TYR cc_start: 0.5325 (OUTLIER) cc_final: 0.3143 (p90)
REVERT: R   43 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.5540 (t80)
REVERT: R   83 MET cc_start: 0.6854 (tpp) cc_final: 0.6059 (ttp)
REVERT: R  178 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.6007 (mt)
REVERT: R  235 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6869 (tp-100)
REVERT: R  285 MET cc_start: 0.7467 (ttm) cc_final: 0.7160 (mtp)
REVERT: R  290 MET cc_start: 0.6284 (tpp) cc_final: 0.5852 (mmm)
REVERT: R  297 PHE cc_start: 0.6444 (m-80) cc_final: 0.6130 (m-80)
  outliers start: 29
  outliers final: 15
  residues processed: 109
  average time/residue: 1.0404
  time to fit residues: 122.3208
Evaluate side-chains
  110 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
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 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  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:   10.0000
   chunk 45 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 67 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4653 r_free = 0.4653 target = 0.219806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.174536 restraints weight = 7493.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 2.47
r_work: 0.3905 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6555
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8222  Z= 0.217
  Angle     :  0.557   6.510  11124  Z= 0.301
  Chirality :  0.042   0.168   1256
  Planarity :  0.004   0.049   1411
  Dihedral  :  4.769  36.330   1120
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.05 %
    Favored  : 79.41 %
  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:  0.21 (0.27), residues: 1001
  helix:  1.25 (0.26), residues: 394
  sheet: -0.46 (0.33), residues: 230
  loop : -0.53 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 251 
 HIS   0.006   0.001   HIS A 324 
 PHE   0.021   0.002   PHE A 199 
 TYR   0.013   0.001   TYR R  72 
 ARG   0.003   0.000   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
  118 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 87
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A  235 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4977 (mm-30)
REVERT: A  256 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6538 (mp)
REVERT: B   96 ARG cc_start: 0.7988 (mtp180) cc_final: 0.7558 (mmp-170)
REVERT: B  218 CYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7286 (t)
REVERT: B  220 GLN cc_start: 0.6935 (mp10) cc_final: 0.5639 (tm-30)
REVERT: B  222 PHE cc_start: 0.5755 (m-80) cc_final: 0.5466 (m-80)
REVERT: G   21 MET cc_start: 0.5079 (ptp) cc_final: 0.4442 (mtt)
REVERT: N  117 TYR cc_start: 0.5319 (OUTLIER) cc_final: 0.3184 (p90)
REVERT: R   43 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5421 (t80)
REVERT: R   83 MET cc_start: 0.6706 (tpp) cc_final: 0.5933 (ttp)
REVERT: R  178 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5917 (mt)
REVERT: R  235 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6762 (tp-100)
REVERT: R  285 MET cc_start: 0.7402 (ttm) cc_final: 0.7045 (mtp)
REVERT: R  297 PHE cc_start: 0.6452 (m-80) cc_final: 0.6162 (m-80)
  outliers start: 31
  outliers final: 16
  residues processed: 105
  average time/residue: 0.9801
  time to fit residues: 111.0055
Evaluate side-chains
  108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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  256 LEU
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0070
   chunk 87 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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**
N  82 GLN
N  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.220540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.164427 restraints weight = 7553.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 1.96
r_work: 0.3935 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3790 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8222  Z= 0.198
  Angle     :  0.544   8.461  11124  Z= 0.293
  Chirality :  0.042   0.167   1256
  Planarity :  0.004   0.049   1411
  Dihedral  :  4.684  34.730   1120
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.73 %
    Favored  : 79.29 %
  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:  0.28 (0.27), residues: 1001
  helix:  1.34 (0.27), residues: 394
  sheet: -0.43 (0.33), residues: 229
  loop : -0.54 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 251 
 HIS   0.006   0.001   HIS A 324 
 PHE   0.016   0.002   PHE A 199 
 TYR   0.015   0.001   TYR R  72 
 ARG   0.003   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
  112 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.5653 (OUTLIER) cc_final: 0.4946 (mm-30)
REVERT: B   96 ARG cc_start: 0.8142 (mtp180) cc_final: 0.7587 (mmp-170)
REVERT: B  218 CYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7399 (t)
REVERT: B  220 GLN cc_start: 0.6932 (mp10) cc_final: 0.5614 (tm-30)
REVERT: B  222 PHE cc_start: 0.5839 (m-80) cc_final: 0.5516 (m-80)
REVERT: G   21 MET cc_start: 0.5019 (ptp) cc_final: 0.4422 (mtt)
REVERT: N  117 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.3241 (p90)
REVERT: R   43 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5352 (t80)
REVERT: R   83 MET cc_start: 0.6791 (tpp) cc_final: 0.6024 (ttp)
REVERT: R   94 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.6139 (mp)
REVERT: R  178 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5805 (mt)
REVERT: R  235 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6904 (tp-100)
REVERT: R  285 MET cc_start: 0.7427 (ttm) cc_final: 0.7102 (mtp)
REVERT: R  290 MET cc_start: 0.6228 (tpp) cc_final: 0.5785 (mmm)
REVERT: R  297 PHE cc_start: 0.6430 (m-80) cc_final: 0.6109 (m-80)
  outliers start: 26
  outliers final: 16
  residues processed: 103
  average time/residue: 0.9657
  time to fit residues: 107.3451
Evaluate side-chains
  105 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   84 ASN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0970
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4657 r_free = 0.4657 target = 0.220161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.164323 restraints weight = 7428.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.4118 rms_B_bonded: 1.93
r_work: 0.3935 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3790 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.2018

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= 0.214
  Angle     :  0.559   9.489  11124  Z= 0.301
  Chirality :  0.042   0.178   1256
  Planarity :  0.004   0.049   1411
  Dihedral  :  4.716  34.255   1120
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.96 %
    Favored  : 79.18 %
  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:  0.27 (0.27), residues: 1001
  helix:  1.31 (0.26), residues: 394
  sheet: -0.45 (0.33), residues: 230
  loop : -0.49 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 332 
 HIS   0.006   0.001   HIS A 324 
 PHE   0.025   0.002   PHE A 199 
 TYR   0.016   0.001   TYR R  72 
 ARG   0.003   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
  108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A  235 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.4976 (mm-30)
REVERT: B   45 MET cc_start: 0.6479 (tpp) cc_final: 0.6273 (tpp)
REVERT: B   96 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7578 (mmp-170)
REVERT: B  218 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7362 (t)
REVERT: B  220 GLN cc_start: 0.6961 (mp10) cc_final: 0.5653 (tm-30)
REVERT: B  222 PHE cc_start: 0.5860 (m-80) cc_final: 0.5536 (m-80)
REVERT: G   21 MET cc_start: 0.5051 (ptp) cc_final: 0.4443 (mtt)
REVERT: N  117 TYR cc_start: 0.5545 (OUTLIER) cc_final: 0.3262 (p90)
REVERT: R   43 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5449 (t80)
REVERT: R   83 MET cc_start: 0.6787 (tpp) cc_final: 0.6020 (ttp)
REVERT: R   94 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.6161 (mp)
REVERT: R  178 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.5867 (mt)
REVERT: R  235 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6900 (tp-100)
REVERT: R  285 MET cc_start: 0.7441 (ttm) cc_final: 0.7119 (mtp)
REVERT: R  297 PHE cc_start: 0.6454 (m-80) cc_final: 0.6130 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 100
  average time/residue: 1.3775
  time to fit residues: 148.1785
Evaluate side-chains
  106 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    0.0670
   chunk 80 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0670
   chunk 50 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.5056

-------------------------------------------------------------------------------
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 = 0.4676 r_free = 0.4676 target = 0.222422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.176313 restraints weight = 7494.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.4235 rms_B_bonded: 2.57
r_work: 0.3907 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8222  Z= 0.172
  Angle     :  0.532  10.049  11124  Z= 0.286
  Chirality :  0.041   0.165   1256
  Planarity :  0.004   0.049   1411
  Dihedral  :  4.551  32.598   1120
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.31 %
    Favored  : 79.06 %
  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:  0.40 (0.27), residues: 1001
  helix:  1.49 (0.27), residues: 394
  sheet: -0.39 (0.33), residues: 227
  loop : -0.51 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 332 
 HIS   0.005   0.001   HIS A 324 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.016   0.001   TYR R  72 
 ARG   0.003   0.000   ARG A 209 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13887.17 seconds
wall clock time: 240 minutes 34.07 seconds (14434.07 seconds total)