Starting phenix.real_space_refine
on Thu Feb 13 11:44:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8j_34549/02_2025/8h8j_34549_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8j_34549/02_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_34549/02_2025/8h8j_34549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8j_34549/02_2025/8h8j_34549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8j_34549/02_2025/8h8j_34549_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8j_34549/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.11, per 1000 atoms: 0.58
  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: 2.40
  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: 1.01
  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: 2.58

  Time building geometry restraints manager: 2.70 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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.170
  Find NCS groups from input model:        0.080
  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:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.680
-------------------------------------------------------------------------------
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  : 0.750 
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: 0.2375
  time to fit residues: 84.7320
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  : 0.900 
-------------------------------------------------------------------------------
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 = 0.149159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.135092 restraints weight = 12386.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.95
r_work: 0.3580 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
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  : 1.073 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7637 (mtmm)
REVERT: A   51 ILE cc_start: 0.8659 (mm) cc_final: 0.8375 (mt)
REVERT: B   25 CYS cc_start: 0.7865 (m) cc_final: 0.7575 (m)
REVERT: B   86 THR cc_start: 0.7700 (p) cc_final: 0.7454 (p)
REVERT: B  117 LEU cc_start: 0.7980 (mt) cc_final: 0.7699 (mt)
REVERT: B  124 TYR cc_start: 0.8329 (m-80) cc_final: 0.7722 (m-80)
REVERT: B  139 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7432 (pp)
REVERT: B  297 TRP cc_start: 0.8333 (m100) cc_final: 0.8041 (m100)
REVERT: B  303 ASP cc_start: 0.7498 (p0) cc_final: 0.7170 (p0)
REVERT: B  340 ASN cc_start: 0.7548 (m110) cc_final: 0.7228 (t0)
REVERT: C   90 GLN cc_start: 0.8202 (mt0) cc_final: 0.7959 (mt0)
REVERT: C  102 MET cc_start: 0.7445 (tpt) cc_final: 0.7002 (tpt)
REVERT: G   21 MET cc_start: 0.8163 (tmm) cc_final: 0.7951 (tmm)
REVERT: G   44 HIS cc_start: 0.8402 (m90) cc_final: 0.8161 (m90)
REVERT: H  156 SER cc_start: 0.8027 (m) cc_final: 0.7718 (t)
  outliers start: 27
  outliers final: 13
  residues processed: 227
  average time/residue: 0.2403
  time to fit residues: 73.2958
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  : 0.978 
-------------------------------------------------------------------------------
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:    0.5980
   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:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3756 r_free = 0.3756 target = 0.136421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.121247 restraints weight = 12367.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.02
r_work: 0.3460 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9024  Z= 0.277
  Angle     :  0.565   5.757  12265  Z= 0.293
  Chirality :  0.042   0.160   1425
  Planarity :  0.004   0.055   1536
  Dihedral  :  6.057  58.424   1447
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 13.81 %
    Favored  : 81.88 %
  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:  0.47 (0.26), residues: 1123
  helix:  1.86 (0.27), residues: 394
  sheet:  0.04 (0.29), residues: 281
  loop : -0.88 (0.31), residues: 448

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   0.024   0.002   PHE H  29 
 TYR   0.017   0.002   TYR H  59 
 ARG   0.007   0.001   ARG C 123 

*********************** 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
  258 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 218
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7812 (mtmm)
REVERT: B   74 SER cc_start: 0.8595 (t) cc_final: 0.8377 (t)
REVERT: B   88 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7939 (m110)
REVERT: B  110 ASN cc_start: 0.8095 (m-40) cc_final: 0.7795 (m110)
REVERT: B  134 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7865 (mtm110)
REVERT: B  170 ASP cc_start: 0.7084 (p0) cc_final: 0.6871 (p0)
REVERT: B  243 THR cc_start: 0.7494 (p) cc_final: 0.7272 (p)
REVERT: B  273 ILE cc_start: 0.8026 (mm) cc_final: 0.7717 (mp)
REVERT: B  303 ASP cc_start: 0.7698 (p0) cc_final: 0.7303 (p0)
REVERT: B  331 SER cc_start: 0.8388 (p) cc_final: 0.8087 (p)
REVERT: C   21 LEU cc_start: 0.7683 (tp) cc_final: 0.7405 (tp)
REVERT: C   90 GLN cc_start: 0.8302 (mt0) cc_final: 0.7988 (mt0)
REVERT: C  102 MET cc_start: 0.7449 (tpt) cc_final: 0.6908 (tpt)
REVERT: C  173 MET cc_start: 0.7448 (mmm) cc_final: 0.7101 (mmm)
REVERT: C  177 LEU cc_start: 0.7658 (mt) cc_final: 0.7413 (mm)
REVERT: C  279 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7019 (mtm)
  outliers start: 40
  outliers final: 22
  residues processed: 238
  average time/residue: 0.2188
  time to fit residues: 70.5461
Evaluate side-chains
  236 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
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  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   88 ASN
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:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0030
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
B  75 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 = 0.3744 r_free = 0.3744 target = 0.135607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.120527 restraints weight = 12293.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.99
r_work: 0.3458 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9024  Z= 0.248
  Angle     :  0.544   6.244  12265  Z= 0.282
  Chirality :  0.041   0.156   1425
  Planarity :  0.004   0.051   1536
  Dihedral  :  5.825  56.430   1447
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.50 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.61 (0.26), residues: 1123
  helix:  2.02 (0.27), residues: 389
  sheet:  0.12 (0.29), residues: 280
  loop : -0.82 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS C 234 
 PHE   0.019   0.002   PHE H  29 
 TYR   0.018   0.002   TYR H 190 
 ARG   0.005   0.001   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
  260 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 222
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7826 (mtmm)
REVERT: A  217 VAL cc_start: 0.8667 (p) cc_final: 0.8332 (m)
REVERT: B   27 ASP cc_start: 0.7761 (p0) cc_final: 0.7559 (p0)
REVERT: B   32 GLN cc_start: 0.7727 (mt0) cc_final: 0.7323 (mt0)
REVERT: B   66 ASP cc_start: 0.8027 (p0) cc_final: 0.7812 (p0)
REVERT: B   74 SER cc_start: 0.8629 (t) cc_final: 0.8080 (p)
REVERT: B  110 ASN cc_start: 0.8085 (m-40) cc_final: 0.7814 (m110)
REVERT: B  134 ARG cc_start: 0.8253 (mtm110) cc_final: 0.7924 (mtm110)
REVERT: B  170 ASP cc_start: 0.7093 (p0) cc_final: 0.6887 (p0)
REVERT: B  303 ASP cc_start: 0.7704 (p0) cc_final: 0.7311 (p0)
REVERT: B  331 SER cc_start: 0.8478 (p) cc_final: 0.8233 (p)
REVERT: C   21 LEU cc_start: 0.7730 (tp) cc_final: 0.7461 (tp)
REVERT: C   53 THR cc_start: 0.7629 (t) cc_final: 0.7100 (p)
REVERT: C   64 VAL cc_start: 0.8004 (t) cc_final: 0.7745 (p)
REVERT: C   90 GLN cc_start: 0.8320 (mt0) cc_final: 0.8006 (mt0)
REVERT: C  102 MET cc_start: 0.7551 (tpt) cc_final: 0.7021 (tpt)
REVERT: C  163 PHE cc_start: 0.8009 (m-10) cc_final: 0.7674 (m-10)
REVERT: C  173 MET cc_start: 0.7292 (mmm) cc_final: 0.7054 (mmm)
REVERT: C  279 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7043 (mtm)
REVERT: H  155 VAL cc_start: 0.8238 (p) cc_final: 0.7985 (m)
  outliers start: 38
  outliers final: 29
  residues processed: 239
  average time/residue: 0.2393
  time to fit residues: 76.7190
Evaluate side-chains
  248 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 218
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
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   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  232 ILE
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0670
   chunk 39 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
C 200 GLN
H 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.120607 restraints weight = 12268.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.90
r_work: 0.3464 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2839

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= 0.235
  Angle     :  0.546   6.538  12265  Z= 0.282
  Chirality :  0.041   0.164   1425
  Planarity :  0.004   0.048   1536
  Dihedral  :  5.760  59.058   1447
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.02 %
    Favored  : 77.99 %
  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:  2.01 (0.27), residues: 392
  sheet:  0.07 (0.29), residues: 280
  loop : -0.75 (0.31), 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  29 
 TYR   0.018   0.002   TYR H 190 
 ARG   0.008   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
  245 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 208
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7835 (mtmm)
REVERT: A   50 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8147 (mtmm)
REVERT: B   32 GLN cc_start: 0.7715 (mt0) cc_final: 0.7317 (mt0)
REVERT: B   74 SER cc_start: 0.8656 (t) cc_final: 0.8089 (p)
REVERT: B  110 ASN cc_start: 0.8086 (m-40) cc_final: 0.7801 (m110)
REVERT: B  134 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7873 (mtm110)
REVERT: B  262 MET cc_start: 0.7338 (mmm) cc_final: 0.7112 (mmm)
REVERT: B  303 ASP cc_start: 0.7707 (p0) cc_final: 0.7306 (p0)
REVERT: B  331 SER cc_start: 0.8427 (p) cc_final: 0.8088 (p)
REVERT: C   21 LEU cc_start: 0.7698 (tp) cc_final: 0.7424 (tp)
REVERT: C   53 THR cc_start: 0.7617 (t) cc_final: 0.7107 (p)
REVERT: C   90 GLN cc_start: 0.8317 (mt0) cc_final: 0.7985 (mt0)
REVERT: C  102 MET cc_start: 0.7507 (tpt) cc_final: 0.7002 (tpt)
REVERT: C  163 PHE cc_start: 0.8018 (m-10) cc_final: 0.7670 (m-10)
REVERT: C  173 MET cc_start: 0.7308 (mmm) cc_final: 0.7019 (mmm)
REVERT: H   32 PHE cc_start: 0.8571 (m-80) cc_final: 0.8049 (m-80)
REVERT: H  155 VAL cc_start: 0.8235 (p) cc_final: 0.7992 (m)
  outliers start: 37
  outliers final: 31
  residues processed: 228
  average time/residue: 0.2267
  time to fit residues: 69.9480
Evaluate side-chains
  234 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
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  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   61 MET
Chi-restraints excluded: chain B residue   67 SER
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  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
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:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0060
   chunk 52 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 100 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0270
   overall best weight:    0.3454

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.136539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.121818 restraints weight = 12284.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.91
r_work: 0.3484 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9024  Z= 0.171
  Angle     :  0.523   8.426  12265  Z= 0.271
  Chirality :  0.040   0.145   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.615  58.708   1447
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.55 %
    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:  0.76 (0.26), residues: 1123
  helix:  2.16 (0.27), residues: 389
  sheet:  0.15 (0.29), residues: 280
  loop : -0.71 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.014   0.001   PHE H  29 
 TYR   0.017   0.001   TYR B 289 
 ARG   0.005   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
  248 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 215
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7812 (mtmm)
REVERT: A   50 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8165 (mtmm)
REVERT: A  217 VAL cc_start: 0.8689 (p) cc_final: 0.8350 (m)
REVERT: A  270 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7876 (mp)
REVERT: B   32 GLN cc_start: 0.7754 (mt0) cc_final: 0.7390 (mt0)
REVERT: B   74 SER cc_start: 0.8599 (t) cc_final: 0.8020 (p)
REVERT: B   86 THR cc_start: 0.8107 (p) cc_final: 0.7533 (t)
REVERT: B  134 ARG cc_start: 0.8238 (mtm110) cc_final: 0.7892 (mtm110)
REVERT: B  303 ASP cc_start: 0.7683 (p0) cc_final: 0.7267 (p0)
REVERT: B  331 SER cc_start: 0.8385 (p) cc_final: 0.8034 (p)
REVERT: C   21 LEU cc_start: 0.7674 (tp) cc_final: 0.7400 (tp)
REVERT: C   90 GLN cc_start: 0.8304 (mt0) cc_final: 0.7959 (mt0)
REVERT: C  102 MET cc_start: 0.7500 (tpt) cc_final: 0.6981 (tpt)
REVERT: C  173 MET cc_start: 0.7381 (mmm) cc_final: 0.7120 (mmm)
REVERT: H   32 PHE cc_start: 0.8508 (m-80) cc_final: 0.8127 (m-80)
REVERT: H  155 VAL cc_start: 0.8255 (p) cc_final: 0.8011 (m)
  outliers start: 33
  outliers final: 24
  residues processed: 231
  average time/residue: 0.2273
  time to fit residues: 70.4677
Evaluate side-chains
  236 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 211
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  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  232 ILE
Chi-restraints excluded: chain B residue  308 LEU
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  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  186 GLN
Chi-restraints excluded: chain H residue  246 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 110 ASN
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.118859 restraints weight = 12296.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.02
r_work: 0.3434 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.3101

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= 0.281
  Angle     :  0.571   9.187  12265  Z= 0.297
  Chirality :  0.042   0.162   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.701  57.227   1446
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.45 %
    Favored  : 77.67 %
  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:  0.73 (0.26), residues: 1123
  helix:  2.07 (0.27), residues: 392
  sheet:  0.12 (0.29), residues: 279
  loop : -0.66 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.036   0.002   PHE C 163 
 TYR   0.018   0.002   TYR H  59 
 ARG   0.007   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
  246 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 210
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7954 (mtmm)
REVERT: A   50 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8186 (mtmm)
REVERT: A  217 VAL cc_start: 0.8689 (p) cc_final: 0.8385 (m)
REVERT: B   32 GLN cc_start: 0.7878 (mt0) cc_final: 0.7483 (mt0)
REVERT: B   59 TYR cc_start: 0.8429 (m-80) cc_final: 0.8217 (m-80)
REVERT: B   74 SER cc_start: 0.8676 (t) cc_final: 0.8106 (p)
REVERT: B   86 THR cc_start: 0.8244 (p) cc_final: 0.7683 (t)
REVERT: B  110 ASN cc_start: 0.8131 (m-40) cc_final: 0.7835 (m110)
REVERT: B  134 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7943 (mtm110)
REVERT: C   21 LEU cc_start: 0.7776 (tp) cc_final: 0.7494 (tp)
REVERT: C   53 THR cc_start: 0.7669 (t) cc_final: 0.7168 (p)
REVERT: C   90 GLN cc_start: 0.8363 (mt0) cc_final: 0.7974 (mt0)
REVERT: C  102 MET cc_start: 0.7538 (tpt) cc_final: 0.7015 (tpt)
REVERT: C  173 MET cc_start: 0.7364 (mmm) cc_final: 0.7030 (mmm)
REVERT: H   32 PHE cc_start: 0.8603 (m-80) cc_final: 0.8107 (m-80)
REVERT: H  155 VAL cc_start: 0.8228 (p) cc_final: 0.7994 (m)
  outliers start: 36
  outliers final: 27
  residues processed: 229
  average time/residue: 0.2382
  time to fit residues: 73.2245
Evaluate side-chains
  230 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 203
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  251 SER
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   43 ILE
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  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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 103 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 220 GLN
B 340 ASN
C  38 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.135549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120738 restraints weight = 12434.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.92
r_work: 0.3451 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3238

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= 0.265
  Angle     :  0.582   8.678  12265  Z= 0.301
  Chirality :  0.042   0.156   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.717  55.903   1446
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.12 %
    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:  0.71 (0.26), residues: 1123
  helix:  1.94 (0.27), residues: 396
  sheet:  0.13 (0.29), residues: 279
  loop : -0.58 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.031   0.002   PHE C 163 
 TYR   0.017   0.002   TYR H 190 
 ARG   0.007   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
  244 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 210
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7981 (mtmm)
REVERT: A   50 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8140 (mtmm)
REVERT: A  217 VAL cc_start: 0.8688 (p) cc_final: 0.8391 (m)
REVERT: B   32 GLN cc_start: 0.7899 (mt0) cc_final: 0.7508 (mt0)
REVERT: B   74 SER cc_start: 0.8716 (t) cc_final: 0.8241 (p)
REVERT: B   86 THR cc_start: 0.8266 (p) cc_final: 0.7716 (t)
REVERT: B  110 ASN cc_start: 0.8110 (m-40) cc_final: 0.7816 (m110)
REVERT: B  134 ARG cc_start: 0.8301 (mtm110) cc_final: 0.7953 (mtm110)
REVERT: B  156 GLN cc_start: 0.8271 (mt0) cc_final: 0.8024 (mt0)
REVERT: B  303 ASP cc_start: 0.7820 (p0) cc_final: 0.7498 (p0)
REVERT: C   21 LEU cc_start: 0.7750 (tp) cc_final: 0.7470 (tp)
REVERT: C   53 THR cc_start: 0.7729 (t) cc_final: 0.7239 (p)
REVERT: C   90 GLN cc_start: 0.8355 (mt0) cc_final: 0.8149 (mt0)
REVERT: C  102 MET cc_start: 0.7554 (tpt) cc_final: 0.7019 (tpt)
REVERT: C  173 MET cc_start: 0.7310 (mmm) cc_final: 0.7000 (mmm)
REVERT: H   32 PHE cc_start: 0.8636 (m-80) cc_final: 0.8148 (m-80)
REVERT: H  155 VAL cc_start: 0.8242 (p) cc_final: 0.8028 (m)
  outliers start: 34
  outliers final: 31
  residues processed: 226
  average time/residue: 0.2339
  time to fit residues: 71.3906
Evaluate side-chains
  239 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 208
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  251 SER
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   43 ILE
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  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  246 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0980
   chunk 105 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 220 GLN

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 = 0.136373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.121627 restraints weight = 12348.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.92
r_work: 0.3461 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9024  Z= 0.226
  Angle     :  0.575   9.406  12265  Z= 0.297
  Chirality :  0.041   0.157   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.650  54.656   1446
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.88 %
    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:  0.78 (0.26), residues: 1123
  helix:  2.02 (0.27), residues: 395
  sheet:  0.19 (0.30), residues: 279
  loop : -0.59 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 339 
 HIS   0.006   0.001   HIS C 234 
 PHE   0.026   0.002   PHE C 163 
 TYR   0.015   0.002   TYR H 190 
 ARG   0.007   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
  233 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 203
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7949 (mtmm)
REVERT: A   50 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8107 (mtmm)
REVERT: A  217 VAL cc_start: 0.8697 (p) cc_final: 0.8392 (m)
REVERT: B   32 GLN cc_start: 0.7890 (mt0) cc_final: 0.7528 (mt0)
REVERT: B   74 SER cc_start: 0.8726 (t) cc_final: 0.8246 (p)
REVERT: B   86 THR cc_start: 0.8282 (p) cc_final: 0.7754 (t)
REVERT: B  110 ASN cc_start: 0.8097 (m-40) cc_final: 0.7810 (m110)
REVERT: B  134 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7978 (mtm110)
REVERT: B  156 GLN cc_start: 0.8270 (mt0) cc_final: 0.8033 (mt0)
REVERT: B  303 ASP cc_start: 0.7819 (p0) cc_final: 0.7494 (p0)
REVERT: C   21 LEU cc_start: 0.7744 (tp) cc_final: 0.7465 (tp)
REVERT: C   53 THR cc_start: 0.7743 (t) cc_final: 0.7263 (p)
REVERT: C  102 MET cc_start: 0.7549 (tpt) cc_final: 0.7012 (tpt)
REVERT: C  173 MET cc_start: 0.7340 (mmm) cc_final: 0.7045 (mmm)
REVERT: H   32 PHE cc_start: 0.8592 (m-80) cc_final: 0.8183 (m-80)
REVERT: H  155 VAL cc_start: 0.8261 (p) cc_final: 0.8044 (m)
  outliers start: 30
  outliers final: 30
  residues processed: 216
  average time/residue: 0.2396
  time to fit residues: 69.0461
Evaluate side-chains
  230 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 200
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  251 SER
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   43 ILE
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  308 LEU
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  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  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:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.135501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.120878 restraints weight = 12244.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.90
r_work: 0.3447 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9024  Z= 0.275
  Angle     :  0.601   9.349  12265  Z= 0.310
  Chirality :  0.042   0.156   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.719  53.121   1446
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.66 %
    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:  0.73 (0.26), residues: 1123
  helix:  1.99 (0.27), residues: 392
  sheet:  0.10 (0.29), residues: 279
  loop : -0.56 (0.31), residues: 452

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   0.026   0.002   PHE C 163 
 TYR   0.018   0.002   TYR H  59 
 ARG   0.007   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
  230 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 198
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7997 (mtmm)
REVERT: A   50 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8127 (mtmm)
REVERT: A  217 VAL cc_start: 0.8705 (p) cc_final: 0.8402 (m)
REVERT: B   32 GLN cc_start: 0.7928 (mt0) cc_final: 0.7559 (mt0)
REVERT: B   74 SER cc_start: 0.8755 (t) cc_final: 0.8366 (p)
REVERT: B   86 THR cc_start: 0.8333 (p) cc_final: 0.7838 (t)
REVERT: B  110 ASN cc_start: 0.8135 (m-40) cc_final: 0.7832 (m110)
REVERT: B  134 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7969 (mtm110)
REVERT: B  303 ASP cc_start: 0.7825 (p0) cc_final: 0.7573 (p0)
REVERT: C   21 LEU cc_start: 0.7747 (tp) cc_final: 0.7473 (tp)
REVERT: C   53 THR cc_start: 0.7748 (t) cc_final: 0.7269 (p)
REVERT: C   90 GLN cc_start: 0.8358 (mt0) cc_final: 0.8071 (mt0)
REVERT: C  102 MET cc_start: 0.7533 (tpt) cc_final: 0.6993 (tpt)
REVERT: C  173 MET cc_start: 0.7342 (mmm) cc_final: 0.7043 (mmm)
REVERT: G   32 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8318 (ttpp)
REVERT: H   32 PHE cc_start: 0.8628 (m-80) cc_final: 0.8066 (m-80)
REVERT: H  155 VAL cc_start: 0.8246 (p) cc_final: 0.8028 (m)
  outliers start: 32
  outliers final: 26
  residues processed: 212
  average time/residue: 0.2580
  time to fit residues: 73.0268
Evaluate side-chains
  229 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  251 SER
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  308 LEU
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  263 LYS
Chi-restraints excluded: chain C residue  287 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  186 GLN
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:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 90 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0050
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.136885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.122128 restraints weight = 12219.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.91
r_work: 0.3466 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9024  Z= 0.216
  Angle     :  0.588  10.432  12265  Z= 0.301
  Chirality :  0.041   0.149   1425
  Planarity :  0.004   0.046   1536
  Dihedral  :  5.606  51.623   1446
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.42 %
    Favored  : 77.67 %
  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:  0.83 (0.26), residues: 1123
  helix:  2.06 (0.27), residues: 395
  sheet:  0.10 (0.29), residues: 279
  loop : -0.47 (0.32), residues: 449

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   0.023   0.002   PHE C 163 
 TYR   0.016   0.002   TYR H 190 
 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: 4940.35 seconds
wall clock time: 88 minutes 18.20 seconds (5298.20 seconds total)