Starting phenix.real_space_refine
on Thu Mar 13 14:15:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8j_34549/03_2025/8h8j_34549_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8j_34549/03_2025/8h8j_34549.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h8j_34549/03_2025/8h8j_34549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8j_34549/03_2025/8h8j_34549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8j_34549/03_2025/8h8j_34549_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8j_34549/03_2025/8h8j_34549_neut.cif"
  }
  resolution = 3.2
  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=   0.025
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      63      5.16       5
     Cl      1      4.86       5
     C    5648      2.51       5
     N    1511      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8842
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1842
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 3, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2553
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 2191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2191
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 271}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "G"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 417
          Classifications: {'peptide': 59}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "H"
      Number of atoms: 1733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1733
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "C"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 106
          Unusual residues: {' CA': 1, 'CLR': 3, 'WYB': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.67, per 1000 atoms: 0.64
  Number of scatterers: 8842
  At special positions: 0
  Unit cell: (105.04, 113.36, 127.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     Cl      1     17.00
     S      63     16.00
     O    1618      8.00
     N    1511      7.00
     C    5648      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  89 " - pdb=" SG  CYS C 162 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      36.1% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 48
      removed outlier: 3.655A  pdb=" N   THR A  43 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TYR A  44 " --> pdb=" O   ARG A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 73
      removed outlier: 3.815A  pdb=" N   ILE A  70 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ILE A  71 " --> pdb=" O   GLN A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.663A  pdb=" N   PHE A 238 " --> pdb=" O   PHE A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.898A  pdb=" N   GLN A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 335
      removed outlier: 3.665A  pdb=" N   ARG A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 375
      removed outlier: 3.619A  pdb=" N   LEU A 358 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 16 through 45
      removed outlier: 4.136A  pdb=" N   LEU C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 79
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'C' and resid 86 through 119
    Processing helix  chain 'C' and resid 121 through 125
      removed outlier: 3.613A  pdb=" N   ARG C 125 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 158
      removed outlier: 3.535A  pdb=" N   GLN C 157 " --> pdb=" O   LEU C 153 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU C 158 " --> pdb=" O   LEU C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 179
      removed outlier: 3.657A  pdb=" N   LEU C 177 " --> pdb=" O   MET C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 198
    Processing helix  chain 'C' and resid 205 through 241
      Proline residue:  C 232  - end of helix
      removed outlier: 3.869A  pdb=" N   LEU C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 267
      removed outlier: 3.983A  pdb=" N   THR C 253 " --> pdb=" O   ALA C 249 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS C 263 " --> pdb=" O   TYR C 259 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU C 264 " --> pdb=" O   ILE C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 272
    Processing helix  chain 'C' and resid 280 through 288
      removed outlier: 3.642A  pdb=" N   GLN C 284 " --> pdb=" O   ALA C 280 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 4.575A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.171A  pdb=" N   VAL A  49 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   VAL A 222 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A  51 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LYS A  50 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   LEU A 245 " --> pdb=" O   LYS A  50 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LEU A  52 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   LEU A 247 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU A  54 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 8.723A  pdb=" N   SER A 249 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.870A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.712A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.881A  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: 6.799A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.637A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.045A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.601A  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: 6.896A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.393A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.803A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.275A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148
      removed outlier: 4.359A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1242 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: 2.75

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1416
        1.27 -     1.41: 2239
        1.41 -     1.54: 5262
        1.54 -     1.68: 17
        1.68 -     1.81: 90
  Bond restraints: 9024
  Sorted by residual:
  bond pdb=" C02 WYB C 401 "
       pdb=" C03 WYB C 401 "
    ideal  model  delta    sigma   weight residual
    1.427  1.528 -0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" C07 WYB C 401 "
       pdb=" N06 WYB C 401 "
    ideal  model  delta    sigma   weight residual
    1.361  1.450 -0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" C16 WYB C 401 "
       pdb=" N15 WYB C 401 "
    ideal  model  delta    sigma   weight residual
    1.363  1.447 -0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" C12 WYB C 401 "
       pdb="CL13 WYB C 401 "
    ideal  model  delta    sigma   weight residual
    1.727  1.781 -0.054 2.00e-02 2.50e+03 7.23e+00
  bond pdb=" CA  THR C 166 "
       pdb=" C   THR C 166 "
    ideal  model  delta    sigma   weight residual
    1.527  1.489  0.038 1.42e-02 4.96e+03 7.11e+00
  ... (remaining 9019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 12037
        2.07 -     4.14: 179
        4.14 -     6.21: 33
        6.21 -     8.27: 11
        8.27 -    10.34: 5
  Bond angle restraints: 12265
  Sorted by residual:
  angle pdb=" N   HIS C 168 "
        pdb=" CA  HIS C 168 "
        pdb=" C   HIS C 168 "
      ideal   model   delta    sigma   weight residual
     108.63   98.29   10.34 1.60e+00 3.91e-01 4.18e+01
  angle pdb=" N   ASN C 169 "
        pdb=" CA  ASN C 169 "
        pdb=" C   ASN C 169 "
      ideal   model   delta    sigma   weight residual
     110.33  118.02   -7.69 1.29e+00 6.01e-01 3.55e+01
  angle pdb=" N   ASN C 171 "
        pdb=" CA  ASN C 171 "
        pdb=" C   ASN C 171 "
      ideal   model   delta    sigma   weight residual
     114.75  108.38    6.37 1.26e+00 6.30e-01 2.56e+01
  angle pdb=" N   SER C 172 "
        pdb=" CA  SER C 172 "
        pdb=" C   SER C 172 "
      ideal   model   delta    sigma   weight residual
     112.45  106.03    6.42 1.39e+00 5.18e-01 2.13e+01
  angle pdb=" C   THR C  83 "
        pdb=" N   SER C  84 "
        pdb=" CA  SER C  84 "
      ideal   model   delta    sigma   weight residual
     121.90  116.43    5.47 1.26e+00 6.30e-01 1.89e+01
  ... (remaining 12260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 5220
       17.56 -    35.12: 202
       35.12 -    52.68: 51
       52.68 -    70.25: 14
       70.25 -    87.81: 2
  Dihedral angle restraints: 5489
    sinusoidal: 2188
      harmonic: 3301
  Sorted by residual:
  dihedral pdb=" CB  CYS C  89 "
           pdb=" SG  CYS C  89 "
           pdb=" SG  CYS C 162 "
           pdb=" CB  CYS C 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.27   58.27     1      1.00e+01 1.00e-02 4.55e+01
  dihedral pdb=" CA  ASP C  82 "
           pdb=" CB  ASP C  82 "
           pdb=" CG  ASP C  82 "
           pdb=" OD1 ASP C  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.76   55.76     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  MET C 173 "
           pdb=" CB  MET C 173 "
           pdb=" CG  MET C 173 "
           pdb=" SD  MET C 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.13  -59.87     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5486 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1172
       0.048 -    0.096: 190
       0.096 -    0.144: 52
       0.144 -    0.192: 5
       0.192 -    0.240: 6
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" CA  ASN C 169 "
            pdb=" N   ASN C 169 "
            pdb=" C   ASN C 169 "
            pdb=" CB  ASN C 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" C13 CLR C 404 "
            pdb=" C12 CLR C 404 "
            pdb=" C14 CLR C 404 "
            pdb=" C17 CLR C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.70   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" C13 CLR C 405 "
            pdb=" C12 CLR C 405 "
            pdb=" C14 CLR C 405 "
            pdb=" C17 CLR C 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.71   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1422 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO B 236 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 335 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.45e+00
        pdb=" C   ARG A 335 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ARG A 335 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A 336 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 217 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.71e+00
        pdb=" N   PRO A 218 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 218 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 218 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 57
        2.53 -     3.12: 6660
        3.12 -     3.72: 14019
        3.72 -     4.31: 19564
        4.31 -     4.90: 32854
  Nonbonded interactions: 73154
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 332 "
            pdb=" NE2 GLN A 338 "
     model   vdw
     1.939 3.120
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR H 175 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   ARG A 335 "
            pdb=" OE1 GLN A 338 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.210 3.040
  ... (remaining 73149 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:             0.950
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.550
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
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      :  0.003   0.101   9024  Z= 0.215
  Angle     :  0.664  10.343  12265  Z= 0.373
  Chirality :  0.042   0.240   1425
  Planarity :  0.003   0.050   1536
  Dihedral  : 10.436  87.807   3354
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.32 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  4.85 %
    Favored  : 92.56 %
  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: -0.78 (0.24), residues: 1123
  helix:  0.76 (0.25), residues: 393
  sheet: -0.54 (0.29), residues: 264
  loop : -1.58 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.000   HIS C 168 
 PHE   0.008   0.001   PHE B 199 
 TYR   0.006   0.001   TYR C 101 
 ARG   0.003   0.000   ARG H  72 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 253
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7407 (mtmm)
REVERT: A   16 SER cc_start: 0.7617 (t) cc_final: 0.7404 (t)
REVERT: A   51 ILE cc_start: 0.8363 (mm) cc_final: 0.8133 (mt)
REVERT: A  244 ILE cc_start: 0.7530 (pt) cc_final: 0.7105 (mt)
REVERT: A  250 SER cc_start: 0.7413 (m) cc_final: 0.7205 (m)
REVERT: A  270 LEU cc_start: 0.8126 (mm) cc_final: 0.7848 (mp)
REVERT: A  299 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6429 (mm-30)
REVERT: B   25 CYS cc_start: 0.7140 (m) cc_final: 0.6864 (m)
REVERT: B   83 ASP cc_start: 0.7790 (t0) cc_final: 0.7557 (t0)
REVERT: B  117 LEU cc_start: 0.7596 (mt) cc_final: 0.7361 (mt)
REVERT: B  124 TYR cc_start: 0.8041 (m-80) cc_final: 0.7513 (m-80)
REVERT: B  271 CYS cc_start: 0.7444 (p) cc_final: 0.7168 (p)
REVERT: B  289 TYR cc_start: 0.8075 (m-80) cc_final: 0.7071 (m-80)
REVERT: B  295 ASN cc_start: 0.7722 (m-40) cc_final: 0.7438 (m110)
REVERT: B  297 TRP cc_start: 0.7838 (m100) cc_final: 0.7451 (m100)
REVERT: B  303 ASP cc_start: 0.7004 (p0) cc_final: 0.6733 (p0)
REVERT: B  333 ASP cc_start: 0.7024 (p0) cc_final: 0.6749 (p0)
REVERT: C   90 GLN cc_start: 0.7743 (mt0) cc_final: 0.7486 (mt0)
REVERT: C  102 MET cc_start: 0.6621 (tpt) cc_final: 0.6246 (tpt)
REVERT: C  123 ARG cc_start: 0.7039 (mtt-85) cc_final: 0.6825 (mtt-85)
REVERT: G   44 HIS cc_start: 0.8144 (m90) cc_final: 0.7894 (m90)
REVERT: H   90 ASP cc_start: 0.7392 (m-30) cc_final: 0.7153 (m-30)
REVERT: H  156 SER cc_start: 0.7551 (m) cc_final: 0.7296 (t)
  outliers start: 24
  outliers final: 11
  residues processed: 269
  average time/residue: 0.2346
  time to fit residues: 84.1506
Evaluate side-chains
  230 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 219
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue  171 ASN
Chi-restraints excluded: chain C residue  173 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  263 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0470
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    0.3980
   chunk 87 optimal weight:    0.3980
   chunk 33 optimal weight:    0.3980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 100 optimal weight:    0.4980
   overall best weight:    0.3478

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
A 339 GLN
A 340 GLN
B 176 GLN
B 220 GLN
B 237 ASN
C  99 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.149160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.135111 restraints weight = 12386.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 1.95
r_work: 0.3579 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9024  Z= 0.179
  Angle     :  0.522   8.692  12265  Z= 0.269
  Chirality :  0.040   0.151   1425
  Planarity :  0.004   0.051   1536
  Dihedral  :  7.449  84.971   1461
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 12.84 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1123
  helix:  1.87 (0.27), residues: 392
  sheet: -0.21 (0.29), residues: 269
  loop : -1.08 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.006   0.001   HIS H 167 
 PHE   0.019   0.001   PHE A 212 
 TYR   0.016   0.001   TYR H 190 
 ARG   0.006   0.001   ARG B  49 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 215
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7639 (mtmm)
REVERT: A   51 ILE cc_start: 0.8658 (mm) cc_final: 0.8374 (mt)
REVERT: B   25 CYS cc_start: 0.7853 (m) cc_final: 0.7566 (m)
REVERT: B   86 THR cc_start: 0.7700 (p) cc_final: 0.7456 (p)
REVERT: B  117 LEU cc_start: 0.7980 (mt) cc_final: 0.7699 (mt)
REVERT: B  124 TYR cc_start: 0.8328 (m-80) cc_final: 0.7722 (m-80)
REVERT: B  139 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7432 (pp)
REVERT: B  297 TRP cc_start: 0.8328 (m100) cc_final: 0.8038 (m100)
REVERT: B  303 ASP cc_start: 0.7498 (p0) cc_final: 0.7171 (p0)
REVERT: B  340 ASN cc_start: 0.7551 (m110) cc_final: 0.7230 (t0)
REVERT: C   90 GLN cc_start: 0.8197 (mt0) cc_final: 0.7955 (mt0)
REVERT: C  102 MET cc_start: 0.7441 (tpt) cc_final: 0.6999 (tpt)
REVERT: G   21 MET cc_start: 0.8158 (tmm) cc_final: 0.7947 (tmm)
REVERT: G   44 HIS cc_start: 0.8402 (m90) cc_final: 0.8160 (m90)
REVERT: H  156 SER cc_start: 0.8025 (m) cc_final: 0.7719 (t)
  outliers start: 27
  outliers final: 13
  residues processed: 227
  average time/residue: 0.2246
  time to fit residues: 68.3874
Evaluate side-chains
  210 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 196
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  186 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0980
   chunk 51 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
A 345 HIS
B 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.136583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.121680 restraints weight = 12383.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.93
r_work: 0.3461 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9024  Z= 0.261
  Angle     :  0.565   6.481  12265  Z= 0.291
  Chirality :  0.042   0.175   1425
  Planarity :  0.004   0.055   1536
  Dihedral  :  6.041  58.262   1447
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 13.92 %
    Favored  : 81.77 %
  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:  0.49 (0.26), residues: 1123
  helix:  1.86 (0.27), residues: 395
  sheet:  0.06 (0.29), residues: 281
  loop : -0.86 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.023   0.002   PHE H  29 
 TYR   0.017   0.002   TYR H 190 
 ARG   0.006   0.001   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 216
  time to evaluate  : 1.510 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7870 (mtmm)
REVERT: B   88 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7960 (m110)
REVERT: B  110 ASN cc_start: 0.8103 (m-40) cc_final: 0.7815 (m110)
REVERT: B  134 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7879 (mtm110)
REVERT: B  170 ASP cc_start: 0.7069 (p0) cc_final: 0.6855 (p0)
REVERT: B  243 THR cc_start: 0.7520 (p) cc_final: 0.7315 (p)
REVERT: B  273 ILE cc_start: 0.8025 (mm) cc_final: 0.7753 (mp)
REVERT: B  295 ASN cc_start: 0.8134 (m-40) cc_final: 0.7901 (m-40)
REVERT: B  303 ASP cc_start: 0.7689 (p0) cc_final: 0.7346 (p0)
REVERT: B  331 SER cc_start: 0.8375 (p) cc_final: 0.8064 (p)
REVERT: C   21 LEU cc_start: 0.7648 (tp) cc_final: 0.7378 (tp)
REVERT: C   90 GLN cc_start: 0.8310 (mt0) cc_final: 0.8008 (mt0)
REVERT: C  102 MET cc_start: 0.7485 (tpt) cc_final: 0.6965 (tpt)
REVERT: C  173 MET cc_start: 0.7438 (mmm) cc_final: 0.7143 (mmm)
REVERT: C  177 LEU cc_start: 0.7648 (mt) cc_final: 0.7394 (mm)
REVERT: C  279 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7023 (mtm)
REVERT: H  175 TYR cc_start: 0.7932 (m-80) cc_final: 0.7501 (m-80)
  outliers start: 40
  outliers final: 22
  residues processed: 235
  average time/residue: 0.2564
  time to fit residues: 81.3062
Evaluate side-chains
  241 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  279 MET
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0870
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
** H 179 GLN ** 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 = 0.3749 r_free = 0.3749 target = 0.135805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.120750 restraints weight = 12279.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.99
r_work: 0.3449 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9024  Z= 0.251
  Angle     :  0.541   6.369  12265  Z= 0.281
  Chirality :  0.041   0.154   1425
  Planarity :  0.004   0.052   1536
  Dihedral  :  5.794  57.642   1447
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.18 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1123
  helix:  2.07 (0.27), residues: 386
  sheet:  0.10 (0.29), residues: 280
  loop : -0.82 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.018   0.002   PHE H  29 
 TYR   0.017   0.002   TYR H 190 
 ARG   0.006   0.000   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 221
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8135 (mtmm)
REVERT: B   32 GLN cc_start: 0.7718 (mt0) cc_final: 0.7301 (mt0)
REVERT: B  110 ASN cc_start: 0.8065 (m-40) cc_final: 0.7785 (m110)
REVERT: B  134 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7874 (mtm110)
REVERT: B  165 THR cc_start: 0.7914 (p) cc_final: 0.6953 (m)
REVERT: B  170 ASP cc_start: 0.7079 (p0) cc_final: 0.6874 (p0)
REVERT: B  303 ASP cc_start: 0.7729 (p0) cc_final: 0.7328 (p0)
REVERT: B  331 SER cc_start: 0.8393 (p) cc_final: 0.8167 (p)
REVERT: C   21 LEU cc_start: 0.7733 (tp) cc_final: 0.7463 (tp)
REVERT: C   53 THR cc_start: 0.7607 (t) cc_final: 0.7066 (p)
REVERT: C   90 GLN cc_start: 0.8304 (mt0) cc_final: 0.7975 (mt0)
REVERT: C  102 MET cc_start: 0.7521 (tpt) cc_final: 0.6982 (tpt)
REVERT: C  163 PHE cc_start: 0.8008 (m-10) cc_final: 0.7654 (m-10)
REVERT: C  173 MET cc_start: 0.7319 (mmm) cc_final: 0.6916 (mmm)
REVERT: C  177 LEU cc_start: 0.7727 (mt) cc_final: 0.7437 (mm)
REVERT: C  279 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7002 (mtm)
REVERT: H   32 PHE cc_start: 0.8562 (m-80) cc_final: 0.8051 (m-80)
REVERT: H  155 VAL cc_start: 0.8223 (p) cc_final: 0.7969 (m)
  outliers start: 38
  outliers final: 28
  residues processed: 238
  average time/residue: 0.2264
  time to fit residues: 72.5590
Evaluate side-chains
  243 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  279 MET
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0000
   chunk 39 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 230 ASN
B 340 ASN
C 200 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.120104 restraints weight = 12281.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.03
r_work: 0.3450 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9024  Z= 0.243
  Angle     :  0.547   6.506  12265  Z= 0.283
  Chirality :  0.041   0.167   1425
  Planarity :  0.004   0.049   1536
  Dihedral  :  5.763  59.897   1447
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 18.02 %
    Favored  : 77.89 %
  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:  0.63 (0.26), residues: 1123
  helix:  1.95 (0.27), residues: 393
  sheet:  0.11 (0.29), residues: 280
  loop : -0.73 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.016   0.002   PHE H  29 
 TYR   0.017   0.002   TYR H 173 
 ARG   0.007   0.000   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 209
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8165 (mtmm)
REVERT: A  217 VAL cc_start: 0.8723 (p) cc_final: 0.8400 (m)
REVERT: B   32 GLN cc_start: 0.7849 (mt0) cc_final: 0.7442 (mt0)
REVERT: B  110 ASN cc_start: 0.8092 (m-40) cc_final: 0.7801 (m110)
REVERT: B  134 ARG cc_start: 0.8282 (mtm110) cc_final: 0.7918 (mtm110)
REVERT: B  170 ASP cc_start: 0.7095 (p0) cc_final: 0.6876 (p0)
REVERT: B  303 ASP cc_start: 0.7726 (p0) cc_final: 0.7310 (p0)
REVERT: B  331 SER cc_start: 0.8393 (p) cc_final: 0.8190 (p)
REVERT: C   21 LEU cc_start: 0.7717 (tp) cc_final: 0.7446 (tp)
REVERT: C   53 THR cc_start: 0.7633 (t) cc_final: 0.7114 (p)
REVERT: C   90 GLN cc_start: 0.8330 (mt0) cc_final: 0.7990 (mt0)
REVERT: C  102 MET cc_start: 0.7542 (tpt) cc_final: 0.7016 (tpt)
REVERT: C  163 PHE cc_start: 0.8038 (m-10) cc_final: 0.7689 (m-10)
REVERT: C  173 MET cc_start: 0.7337 (mmm) cc_final: 0.7043 (mmm)
REVERT: H   32 PHE cc_start: 0.8597 (m-80) cc_final: 0.8097 (m-80)
REVERT: H  155 VAL cc_start: 0.8233 (p) cc_final: 0.7989 (m)
  outliers start: 38
  outliers final: 33
  residues processed: 229
  average time/residue: 0.2322
  time to fit residues: 71.6960
Evaluate side-chains
  234 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 201
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    0.2980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 340 ASN
** H 179 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.134363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.119209 restraints weight = 12253.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.02
r_work: 0.3422 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9024  Z= 0.256
  Angle     :  0.550   6.566  12265  Z= 0.285
  Chirality :  0.041   0.160   1425
  Planarity :  0.004   0.048   1536
  Dihedral  :  5.755  58.267   1447
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.91 %
    Favored  : 78.21 %
  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:  0.65 (0.26), residues: 1123
  helix:  1.98 (0.27), residues: 392
  sheet:  0.10 (0.29), residues: 280
  loop : -0.71 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.015   0.002   PHE H 239 
 TYR   0.018   0.002   TYR B 289 
 ARG   0.006   0.000   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 207
  time to evaluate  : 1.021 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8133 (mtmm)
REVERT: A  217 VAL cc_start: 0.8699 (p) cc_final: 0.8403 (m)
REVERT: A  270 LEU cc_start: 0.8256 (mm) cc_final: 0.7926 (mp)
REVERT: B   32 GLN cc_start: 0.7900 (mt0) cc_final: 0.7504 (mt0)
REVERT: B   86 THR cc_start: 0.8227 (p) cc_final: 0.7600 (t)
REVERT: B  134 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7949 (mtm110)
REVERT: B  230 ASN cc_start: 0.8036 (m-40) cc_final: 0.7798 (m-40)
REVERT: B  331 SER cc_start: 0.8418 (p) cc_final: 0.8209 (p)
REVERT: C   21 LEU cc_start: 0.7759 (tp) cc_final: 0.7486 (tp)
REVERT: C   53 THR cc_start: 0.7662 (t) cc_final: 0.7153 (p)
REVERT: C   90 GLN cc_start: 0.8335 (mt0) cc_final: 0.7980 (mt0)
REVERT: C  102 MET cc_start: 0.7517 (tpt) cc_final: 0.6997 (tpt)
REVERT: C  163 PHE cc_start: 0.8053 (m-10) cc_final: 0.7702 (m-10)
REVERT: C  173 MET cc_start: 0.7379 (mmm) cc_final: 0.7048 (mmm)
REVERT: H   32 PHE cc_start: 0.8591 (m-80) cc_final: 0.8113 (m-80)
REVERT: H  155 VAL cc_start: 0.8225 (p) cc_final: 0.7984 (m)
  outliers start: 36
  outliers final: 30
  residues processed: 226
  average time/residue: 0.2294
  time to fit residues: 69.7317
Evaluate side-chains
  234 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 204
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0060
   chunk 80 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
B 176 GLN
B 220 GLN
B 340 ASN
C  38 ASN
** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.134570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119523 restraints weight = 12282.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.01
r_work: 0.3425 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9024  Z= 0.226
  Angle     :  0.545   7.069  12265  Z= 0.282
  Chirality :  0.041   0.159   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.685  56.934   1447
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 17.80 %
    Favored  : 77.89 %
  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:  0.71 (0.26), residues: 1123
  helix:  2.00 (0.27), residues: 393
  sheet:  0.11 (0.29), residues: 279
  loop : -0.62 (0.32), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.016   0.002   PHE H 239 
 TYR   0.018   0.002   TYR H 173 
 ARG   0.005   0.000   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 205
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8130 (mtmm)
REVERT: A  217 VAL cc_start: 0.8688 (p) cc_final: 0.8400 (m)
REVERT: A  270 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7912 (mp)
REVERT: B   32 GLN cc_start: 0.7892 (mt0) cc_final: 0.7485 (mt0)
REVERT: B   86 THR cc_start: 0.8214 (p) cc_final: 0.7593 (t)
REVERT: B  110 ASN cc_start: 0.8124 (m-40) cc_final: 0.7848 (m110)
REVERT: B  134 ARG cc_start: 0.8314 (mtm110) cc_final: 0.7974 (mtm110)
REVERT: B  331 SER cc_start: 0.8451 (p) cc_final: 0.8244 (p)
REVERT: C   21 LEU cc_start: 0.7753 (tp) cc_final: 0.7472 (tp)
REVERT: C   53 THR cc_start: 0.7682 (t) cc_final: 0.7153 (p)
REVERT: C   90 GLN cc_start: 0.8330 (mt0) cc_final: 0.7963 (mt0)
REVERT: C  102 MET cc_start: 0.7507 (tpt) cc_final: 0.6985 (tpt)
REVERT: C  163 PHE cc_start: 0.8103 (m-10) cc_final: 0.7780 (m-10)
REVERT: C  173 MET cc_start: 0.7400 (mmm) cc_final: 0.7043 (mmm)
REVERT: H   32 PHE cc_start: 0.8598 (m-80) cc_final: 0.8090 (m-80)
REVERT: H  155 VAL cc_start: 0.8232 (p) cc_final: 0.7992 (m)
  outliers start: 40
  outliers final: 34
  residues processed: 225
  average time/residue: 0.2312
  time to fit residues: 70.3633
Evaluate side-chains
  238 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 203
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  170 PHE
Chi-restraints excluded: chain C residue  218 MET
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9990
   chunk 104 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 230 ASN
B 340 ASN
** H 179 GLN ** 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 = 0.3747 r_free = 0.3747 target = 0.136438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.121703 restraints weight = 12429.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.92
r_work: 0.3459 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9024  Z= 0.241
  Angle     :  0.555   8.374  12265  Z= 0.287
  Chirality :  0.041   0.162   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.641  55.866   1446
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 17.37 %
    Favored  : 78.32 %
  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:  0.72 (0.26), residues: 1123
  helix:  1.97 (0.27), residues: 393
  sheet:  0.13 (0.29), residues: 279
  loop : -0.60 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.017   0.002   PHE H 239 
 TYR   0.018   0.002   TYR H 173 
 ARG   0.009   0.000   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 211
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8095 (mtmm)
REVERT: A  217 VAL cc_start: 0.8697 (p) cc_final: 0.8410 (m)
REVERT: A  270 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7922 (mp)
REVERT: B   32 GLN cc_start: 0.7889 (mt0) cc_final: 0.7509 (mt0)
REVERT: B   86 THR cc_start: 0.8241 (p) cc_final: 0.7685 (t)
REVERT: B  110 ASN cc_start: 0.8088 (m-40) cc_final: 0.7807 (m110)
REVERT: B  134 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7987 (mtm110)
REVERT: B  156 GLN cc_start: 0.8281 (mt0) cc_final: 0.8012 (mt0)
REVERT: B  331 SER cc_start: 0.8439 (p) cc_final: 0.8217 (p)
REVERT: C   21 LEU cc_start: 0.7739 (tp) cc_final: 0.7459 (tp)
REVERT: C   53 THR cc_start: 0.7723 (t) cc_final: 0.7226 (p)
REVERT: C  102 MET cc_start: 0.7531 (tpt) cc_final: 0.7001 (tpt)
REVERT: C  163 PHE cc_start: 0.8111 (m-10) cc_final: 0.7774 (m-10)
REVERT: C  173 MET cc_start: 0.7317 (mmm) cc_final: 0.7018 (mmm)
REVERT: H   32 PHE cc_start: 0.8592 (m-80) cc_final: 0.8153 (m-80)
REVERT: H  155 VAL cc_start: 0.8246 (p) cc_final: 0.8027 (m)
  outliers start: 40
  outliers final: 37
  residues processed: 231
  average time/residue: 0.2251
  time to fit residues: 69.8526
Evaluate side-chains
  245 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 207
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  170 PHE
Chi-restraints excluded: chain C residue  218 MET
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  246 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 70 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 230 ASN
** H 179 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.135780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.121073 restraints weight = 12330.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.90
r_work: 0.3448 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9024  Z= 0.263
  Angle     :  0.580   9.781  12265  Z= 0.298
  Chirality :  0.042   0.159   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.683  54.818   1446
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 18.02 %
    Favored  : 77.89 %
  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:  0.67 (0.26), residues: 1123
  helix:  1.88 (0.27), residues: 396
  sheet:  0.11 (0.29), residues: 279
  loop : -0.58 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.015   0.002   PHE H 239 
 TYR   0.020   0.002   TYR H 173 
 ARG   0.008   0.000   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 206
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8096 (mtmm)
REVERT: A  217 VAL cc_start: 0.8681 (p) cc_final: 0.8379 (m)
REVERT: A  270 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7923 (mp)
REVERT: B   32 GLN cc_start: 0.7895 (mt0) cc_final: 0.7523 (mt0)
REVERT: B   86 THR cc_start: 0.8264 (p) cc_final: 0.7722 (t)
REVERT: B  110 ASN cc_start: 0.8103 (m-40) cc_final: 0.7813 (m110)
REVERT: B  134 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7992 (mtm110)
REVERT: B  156 GLN cc_start: 0.8290 (mt0) cc_final: 0.8066 (mt0)
REVERT: B  230 ASN cc_start: 0.7973 (m-40) cc_final: 0.7728 (m-40)
REVERT: B  262 MET cc_start: 0.7286 (mmm) cc_final: 0.7056 (mmm)
REVERT: B  331 SER cc_start: 0.8435 (p) cc_final: 0.8221 (p)
REVERT: C   21 LEU cc_start: 0.7759 (tp) cc_final: 0.7482 (tp)
REVERT: C   53 THR cc_start: 0.7738 (t) cc_final: 0.7242 (p)
REVERT: C  102 MET cc_start: 0.7513 (tpt) cc_final: 0.6985 (tpt)
REVERT: C  163 PHE cc_start: 0.8108 (m-10) cc_final: 0.7761 (m-10)
REVERT: C  173 MET cc_start: 0.7348 (mmm) cc_final: 0.7044 (mmm)
REVERT: G   32 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8329 (ttpp)
REVERT: H   32 PHE cc_start: 0.8612 (m-80) cc_final: 0.8175 (m-80)
REVERT: H  155 VAL cc_start: 0.8241 (p) cc_final: 0.8023 (m)
  outliers start: 38
  outliers final: 36
  residues processed: 225
  average time/residue: 0.2421
  time to fit residues: 73.1378
Evaluate side-chains
  241 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  170 PHE
Chi-restraints excluded: chain C residue  218 MET
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 340 ASN
H 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.120809 restraints weight = 12249.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.89
r_work: 0.3447 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9024  Z= 0.271
  Angle     :  0.594  10.028  12265  Z= 0.307
  Chirality :  0.042   0.157   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.702  52.936   1446
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 17.69 %
    Favored  : 77.89 %
  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:  0.66 (0.26), residues: 1123
  helix:  1.84 (0.27), residues: 395
  sheet:  0.11 (0.29), residues: 279
  loop : -0.56 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.025   0.002   PHE H  29 
 TYR   0.021   0.002   TYR H 173 
 ARG   0.008   0.000   ARG C 164 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 205
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8099 (mtmm)
REVERT: A  217 VAL cc_start: 0.8695 (p) cc_final: 0.8397 (m)
REVERT: A  270 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7926 (mp)
REVERT: B   32 GLN cc_start: 0.7919 (mt0) cc_final: 0.7647 (mt0)
REVERT: B   86 THR cc_start: 0.8325 (p) cc_final: 0.7828 (t)
REVERT: B  110 ASN cc_start: 0.8118 (m-40) cc_final: 0.7829 (m110)
REVERT: B  134 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7974 (mtm110)
REVERT: B  258 ASP cc_start: 0.7712 (t0) cc_final: 0.7470 (t0)
REVERT: B  262 MET cc_start: 0.7199 (mmm) cc_final: 0.6962 (mmm)
REVERT: B  331 SER cc_start: 0.8431 (p) cc_final: 0.8217 (p)
REVERT: C   21 LEU cc_start: 0.7766 (tp) cc_final: 0.7496 (tp)
REVERT: C   53 THR cc_start: 0.7739 (t) cc_final: 0.7250 (p)
REVERT: C  102 MET cc_start: 0.7495 (tpt) cc_final: 0.6953 (tpt)
REVERT: C  163 PHE cc_start: 0.8125 (m-10) cc_final: 0.7783 (m-10)
REVERT: C  173 MET cc_start: 0.7337 (mmm) cc_final: 0.7034 (mmm)
REVERT: G   32 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8318 (ttpp)
REVERT: H   32 PHE cc_start: 0.8596 (m-80) cc_final: 0.8129 (m-80)
REVERT: H  155 VAL cc_start: 0.8239 (p) cc_final: 0.8016 (m)
  outliers start: 41
  outliers final: 34
  residues processed: 227
  average time/residue: 0.2360
  time to fit residues: 71.5850
Evaluate side-chains
  240 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  158 GLU
Chi-restraints excluded: chain C residue  170 PHE
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  263 LYS
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0050
   chunk 90 optimal weight:    0.1980
   chunk 65 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 105 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.121531 restraints weight = 12248.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.89
r_work: 0.3450 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.131   9024  Z= 0.337
  Angle     :  0.979  58.807  12265  Z= 0.562
  Chirality :  0.041   0.182   1425
  Planarity :  0.004   0.045   1536
  Dihedral  :  5.704  52.932   1446
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.31 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.09 %
  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:  0.67 (0.26), residues: 1123
  helix:  1.86 (0.27), residues: 395
  sheet:  0.11 (0.29), residues: 279
  loop : -0.56 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.024   0.002   PHE H  29 
 TYR   0.018   0.002   TYR H 173 
 ARG   0.006   0.000   ARG C 164 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5028.06 seconds
wall clock time: 88 minutes 4.62 seconds (5284.62 seconds total)