Starting phenix.real_space_refine
on Wed Sep 17 14:50:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3h_62015/09_2025/9k3h_62015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3h_62015/09_2025/9k3h_62015.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k3h_62015/09_2025/9k3h_62015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3h_62015/09_2025/9k3h_62015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3h_62015/09_2025/9k3h_62015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3h_62015/09_2025/9k3h_62015.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      71      5.16       5
     C    5606      2.51       5
     N    1524      2.21       5
     O    1634      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8835
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2112
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 265}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "A"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1942
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2590
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 25
    Chain: "G"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 427
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "S"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1764
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 1.93, per 1000 atoms: 0.22
  Number of scatterers: 8835
  At special positions: 0
  Unit cell: (85.68, 118.881, 131.733, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      71     16.00
     O    1634      8.00
     N    1524      7.00
     C    5606      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 264 " - pdb=" SG  CYS R 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 453.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      37.9% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'R' and resid 40 through 64
    Processing helix  chain 'R' and resid 69 through 99
      removed outlier: 4.213A  pdb=" N   GLU R  92 " --> pdb=" O   SER R  88 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   THR R  93 " --> pdb=" O   SER R  89 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   THR R  95 " --> pdb=" O   TRP R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 107 through 109
      No H-bonds generated for 'chain 'R' and resid 107 through 109'
    Processing helix  chain 'R' and resid 110 through 146
      removed outlier: 5.292A  pdb=" N   ILE R 122 " --> pdb=" O   PHE R 118 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   CYS R 123 " --> pdb=" O   ASP R 119 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL R 127 " --> pdb=" O   CYS R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 153
      removed outlier: 3.855A  pdb=" N   TYR R 150 " --> pdb=" O   ALA R 147 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   HIS R 151 " --> pdb=" O   LEU R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 180
    Processing helix  chain 'R' and resid 187 through 221
      removed outlier: 3.982A  pdb=" N   ILE R 191 " --> pdb=" O   ILE R 187 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   MET R 193 " --> pdb=" O   CYS R 189 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA R 196 " --> pdb=" O   SER R 192 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE R 199 " --> pdb=" O   PHE R 195 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU R 201 " --> pdb=" O   MET R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 264
      removed outlier: 4.235A  pdb=" N   GLY R 236 " --> pdb=" O   THR R 232 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   VAL R 246 " --> pdb=" O   MET R 242 " (cutoff:3.500A)
      Proline residue:  R 253  - end of helix
    Processing helix  chain 'R' and resid 267 through 275
    Processing helix  chain 'R' and resid 276 through 295
      removed outlier: 3.598A  pdb=" N   LEU R 283 " --> pdb=" O   MET R 279 " (cutoff:3.500A)
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 311
    Processing helix  chain 'A' and resid 22 through 38
      removed outlier: 3.704A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.856A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   TYR A  63 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 4.073A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 4.181A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.250A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 4.076A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.520A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.943A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 36
      removed outlier: 4.526A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 11
      No H-bonds generated for 'chain 'G' and resid 9 through 11'
    Processing helix  chain 'G' and resid 12 through 25
      removed outlier: 4.028A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 43
      removed outlier: 4.006A  pdb=" N   CYS G  41 " --> pdb=" O   LEU G  37 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLU G  42 " --> pdb=" O   MET G  38 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA G  43 " --> pdb=" O   ALA G  39 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 74 through 76
      No H-bonds generated for 'chain 'S' and resid 74 through 76'
    Processing helix  chain 'S' and resid 191 through 193
      No H-bonds generated for 'chain 'S' and resid 191 through 193'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 4.418A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.513A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.585A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 7.232A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.928A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.633A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.435A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.513A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.672A  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: 6.430A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277
      removed outlier: 3.909A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.634A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.553A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 4.092A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1167 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2876
        1.34 -     1.46: 2181
        1.46 -     1.58: 3851
        1.58 -     1.70: 0
        1.70 -     1.82: 107
  Bond restraints: 9015
  Sorted by residual:
  bond pdb=" CG1 ILE R 136 "
       pdb=" CD1 ILE R 136 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.33e+00
  bond pdb=" CG1 ILE R  58 "
       pdb=" CD1 ILE R  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.13e+00
  bond pdb=" CA  TYR S 235 "
       pdb=" C   TYR S 235 "
    ideal  model  delta    sigma   weight residual
    1.524  1.536 -0.013 1.26e-02 6.30e+03 1.01e+00
  bond pdb=" C   ILE R 187 "
       pdb=" O   ILE R 187 "
    ideal  model  delta    sigma   weight residual
    1.242  1.232  0.010 1.13e-02 7.83e+03 8.41e-01
  bond pdb=" C   VAL R  62 "
       pdb=" O   VAL R  62 "
    ideal  model  delta    sigma   weight residual
    1.241  1.230  0.011 1.19e-02 7.06e+03 8.32e-01
  ... (remaining 9010 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 11922
        1.83 -     3.66: 242
        3.66 -     5.50: 31
        5.50 -     7.33: 5
        7.33 -     9.16: 3
  Bond angle restraints: 12203
  Sorted by residual:
  angle pdb=" N   TYR A 253 "
        pdb=" CA  TYR A 253 "
        pdb=" C   TYR A 253 "
      ideal   model   delta    sigma   weight residual
     114.04  109.14    4.90 1.24e+00 6.50e-01 1.56e+01
  angle pdb=" N   VAL R 186 "
        pdb=" CA  VAL R 186 "
        pdb=" C   VAL R 186 "
      ideal   model   delta    sigma   weight residual
     113.00  108.13    4.87 1.30e+00 5.92e-01 1.40e+01
  angle pdb=" CB  MET R  83 "
        pdb=" CG  MET R  83 "
        pdb=" SD  MET R  83 "
      ideal   model   delta    sigma   weight residual
     112.70  103.54    9.16 3.00e+00 1.11e-01 9.32e+00
  angle pdb=" C   ASN R 278 "
        pdb=" N   MET R 279 "
        pdb=" CA  MET R 279 "
      ideal   model   delta    sigma   weight residual
     121.94  116.02    5.92 2.00e+00 2.50e-01 8.76e+00
  angle pdb=" CB  MET G  21 "
        pdb=" CG  MET G  21 "
        pdb=" SD  MET G  21 "
      ideal   model   delta    sigma   weight residual
     112.70  121.41   -8.71 3.00e+00 1.11e-01 8.44e+00
  ... (remaining 12198 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4942
       17.93 -    35.86: 370
       35.86 -    53.79: 45
       53.79 -    71.71: 8
       71.71 -    89.64: 5
  Dihedral angle restraints: 5370
    sinusoidal: 2082
      harmonic: 3288
  Sorted by residual:
  dihedral pdb=" CA  TYR A 391 "
           pdb=" C   TYR A 391 "
           pdb=" N   GLU A 392 "
           pdb=" CA  GLU A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.14  -29.86     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  PHE R 118 "
           pdb=" C   PHE R 118 "
           pdb=" N   ASP R 119 "
           pdb=" CA  ASP R 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.85   24.15     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.32   20.68     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 5367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 839
       0.032 -    0.065: 356
       0.065 -    0.097: 133
       0.097 -    0.129: 54
       0.129 -    0.162: 6
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  MET R 279 "
            pdb=" N   MET R 279 "
            pdb=" C   MET R 279 "
            pdb=" CB  MET R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.53e-01
  chirality pdb=" CA  TYR A 391 "
            pdb=" N   TYR A 391 "
            pdb=" C   TYR A 391 "
            pdb=" CB  TYR A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.60e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1385 not shown)

  Planarity restraints: 1545
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 222 "   -0.041 5.00e-02 4.00e+02   6.30e-02 6.35e+00
        pdb=" N   PRO R 223 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO R 223 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R 223 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO B 236 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG S 180 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO S 181 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO S 181 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO S 181 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1542 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 200
        2.67 -     3.23: 8899
        3.23 -     3.79: 13945
        3.79 -     4.34: 18720
        4.34 -     4.90: 30748
  Nonbonded interactions: 72512
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN R  54 "
            pdb=" OD2 ASP R  82 "
     model   vdw
     2.116 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" NE2 GLN B 220 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.146 3.120
  nonbonded pdb=" NH2 ARG B  49 "
            pdb=" O   PHE G  61 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OD1 ASP R  82 "
            pdb=" OG  SER R 288 "
     model   vdw
     2.228 3.040
  ... (remaining 72507 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.680
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
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      :  0.004   0.045   9018  Z= 0.173
  Angle     :  0.659   9.160  12209  Z= 0.375
  Chirality :  0.043   0.162   1388
  Planarity :  0.004   0.063   1545
  Dihedral  : 12.795  89.644   3237
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.26), residues: 1115
  helix:  0.44 (0.27), residues: 390
  sheet: -1.23 (0.32), residues: 279
  loop : -1.40 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 213 
 TYR   0.023   0.002   TYR B  59 
 PHE   0.012   0.001   PHE B 234 
 TRP   0.015   0.002   TRP B  99 
 HIS   0.011   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9015)
  covalent geometry    : angle       0.65847 (12203)
  SS BOND              : bond        0.00312 (    3)
  SS BOND              : angle       0.77879 (    6)
  hydrogen bonds       : bond        0.19946 (  411)
  hydrogen bonds       : angle       7.58374 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   52 LEU cc_start: 0.9153 (tp) cc_final: 0.8951 (tm)
REVERT: R  119 ASP cc_start: 0.7860 (p0) cc_final: 0.7634 (p0)
REVERT: R  149 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7353 (mmm160)
REVERT: R  235 GLN cc_start: 0.7924 (tt0) cc_final: 0.7662 (tt0)
REVERT: R  256 LEU cc_start: 0.9027 (tt) cc_final: 0.8765 (tt)
REVERT: R  274 MET cc_start: 0.8404 (mmm) cc_final: 0.8189 (mmm)
REVERT: R  297 PHE cc_start: 0.7745 (t80) cc_final: 0.7359 (t80)
REVERT: A  378 ASP cc_start: 0.8607 (m-30) cc_final: 0.8395 (m-30)
REVERT: A  392 GLU cc_start: 0.7613 (tp30) cc_final: 0.7397 (tp30)
REVERT: B   14 LEU cc_start: 0.9404 (mt) cc_final: 0.9177 (mt)
REVERT: B  217 MET cc_start: 0.8630 (pmm) cc_final: 0.8201 (pmm)
REVERT: G   17 GLU cc_start: 0.8943 (mp0) cc_final: 0.8524 (mp0)
REVERT: G   32 LYS cc_start: 0.8559 (tptm) cc_final: 0.8314 (tppp)
REVERT: G   48 ASP cc_start: 0.8058 (t0) cc_final: 0.7732 (t70)
REVERT: S   13 GLN cc_start: 0.8952 (tp40) cc_final: 0.8732 (pp30)
REVERT: S   90 ASP cc_start: 0.8958 (m-30) cc_final: 0.8705 (m-30)
REVERT: S   93 MET cc_start: 0.8256 (tpt) cc_final: 0.7991 (tpt)
  outliers start: 0
  outliers final: 1
  residues processed: 214
  average time/residue: 0.6412
  time to fit residues: 144.6924
Evaluate side-chains
  168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0470
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.4980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.114775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.083332 restraints weight = 17671.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 3.59
r_work: 0.3049 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9018  Z= 0.135
  Angle     :  0.661  10.190  12209  Z= 0.343
  Chirality :  0.044   0.158   1388
  Planarity :  0.005   0.047   1545
  Dihedral  :  4.990  25.640   1233
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.15 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.25), residues: 1115
  helix:  0.41 (0.26), residues: 408
  sheet: -0.90 (0.31), residues: 281
  loop : -1.63 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  38 
 TYR   0.010   0.001   TYR R 180 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.007   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9015)
  covalent geometry    : angle       0.66055 (12203)
  SS BOND              : bond        0.00385 (    3)
  SS BOND              : angle       0.95372 (    6)
  hydrogen bonds       : bond        0.04435 (  411)
  hydrogen bonds       : angle       5.21755 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 194
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   52 LEU cc_start: 0.9076 (tp) cc_final: 0.8863 (tm)
REVERT: R   82 ASP cc_start: 0.8087 (t70) cc_final: 0.7841 (t70)
REVERT: R  119 ASP cc_start: 0.7908 (p0) cc_final: 0.7679 (p0)
REVERT: R  235 GLN cc_start: 0.7947 (tt0) cc_final: 0.7675 (tt0)
REVERT: R  274 MET cc_start: 0.8539 (mmm) cc_final: 0.8223 (mmm)
REVERT: R  297 PHE cc_start: 0.7771 (t80) cc_final: 0.7420 (t80)
REVERT: R  301 GLU cc_start: 0.8563 (pm20) cc_final: 0.7856 (pp20)
REVERT: A   21 GLU cc_start: 0.7560 (mp0) cc_final: 0.6609 (mp0)
REVERT: A   63 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7024 (p90)
REVERT: A  207 ILE cc_start: 0.8961 (mt) cc_final: 0.8714 (mm)
REVERT: A  392 GLU cc_start: 0.8307 (tp30) cc_final: 0.7815 (tp30)
REVERT: B    9 GLN cc_start: 0.9452 (tp-100) cc_final: 0.9124 (tm-30)
REVERT: B   10 GLU cc_start: 0.9634 (mt-10) cc_final: 0.9387 (pt0)
REVERT: B   20 ASP cc_start: 0.9418 (p0) cc_final: 0.9208 (p0)
REVERT: B   59 TYR cc_start: 0.8554 (m-80) cc_final: 0.7685 (m-80)
REVERT: B   74 SER cc_start: 0.8286 (t) cc_final: 0.8026 (t)
REVERT: B  217 MET cc_start: 0.8710 (pmm) cc_final: 0.8314 (pmm)
REVERT: B  262 MET cc_start: 0.8182 (mmm) cc_final: 0.7956 (mmm)
REVERT: B  339 TRP cc_start: 0.8239 (m100) cc_final: 0.7912 (m100)
REVERT: G   13 ARG cc_start: 0.9450 (ptp-110) cc_final: 0.9025 (ptp-110)
REVERT: G   17 GLU cc_start: 0.9153 (mp0) cc_final: 0.8917 (mp0)
REVERT: G   31 SER cc_start: 0.8572 (t) cc_final: 0.8179 (m)
REVERT: G   32 LYS cc_start: 0.8585 (tptm) cc_final: 0.8330 (tppp)
REVERT: G   48 ASP cc_start: 0.8004 (t0) cc_final: 0.7436 (t0)
REVERT: S   13 GLN cc_start: 0.9177 (tp40) cc_final: 0.8603 (pp30)
REVERT: S   90 ASP cc_start: 0.9258 (m-30) cc_final: 0.8830 (m-30)
REVERT: S   93 MET cc_start: 0.8865 (tpt) cc_final: 0.8636 (tpt)
  outliers start: 21
  outliers final: 5
  residues processed: 198
  average time/residue: 0.5710
  time to fit residues: 120.5807
Evaluate side-chains
  174 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 168
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 109 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0050
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.9398

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.110200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.078423 restraints weight = 17730.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 3.54
r_work: 0.2953 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9018  Z= 0.234
  Angle     :  0.695   9.774  12209  Z= 0.361
  Chirality :  0.046   0.184   1388
  Planarity :  0.004   0.039   1545
  Dihedral  :  5.142  25.349   1231
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.56 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.25), residues: 1115
  helix:  0.56 (0.27), residues: 399
  sheet: -0.83 (0.31), residues: 288
  loop : -1.59 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG S 160 
 TYR   0.013   0.002   TYR S  59 
 PHE   0.013   0.002   PHE S 239 
 TRP   0.016   0.002   TRP B  99 
 HIS   0.007   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 9015)
  covalent geometry    : angle       0.69523 (12203)
  SS BOND              : bond        0.00357 (    3)
  SS BOND              : angle       0.88300 (    6)
  hydrogen bonds       : bond        0.04555 (  411)
  hydrogen bonds       : angle       5.04425 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ASP cc_start: 0.8019 (t70) cc_final: 0.7802 (t70)
REVERT: R  119 ASP cc_start: 0.7935 (p0) cc_final: 0.7681 (p0)
REVERT: R  149 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7493 (mmm160)
REVERT: R  235 GLN cc_start: 0.8042 (tt0) cc_final: 0.7737 (tt0)
REVERT: R  273 PHE cc_start: 0.9310 (t80) cc_final: 0.8936 (t80)
REVERT: R  274 MET cc_start: 0.8503 (mmm) cc_final: 0.8191 (mmm)
REVERT: R  279 MET cc_start: 0.8061 (pmm) cc_final: 0.6926 (ttt)
REVERT: R  297 PHE cc_start: 0.7889 (t80) cc_final: 0.7423 (t80)
REVERT: A   27 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7964 (mm-30)
REVERT: A   63 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.6922 (p90)
REVERT: A  207 ILE cc_start: 0.9042 (mt) cc_final: 0.8842 (mm)
REVERT: A  392 GLU cc_start: 0.8259 (tp30) cc_final: 0.7855 (tp30)
REVERT: B   45 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8514 (mpp)
REVERT: B   59 TYR cc_start: 0.8645 (m-80) cc_final: 0.7994 (m-80)
REVERT: B  217 MET cc_start: 0.8578 (pmm) cc_final: 0.8160 (pmm)
REVERT: B  298 ASP cc_start: 0.7946 (t70) cc_final: 0.7699 (t70)
REVERT: G   17 GLU cc_start: 0.9119 (mp0) cc_final: 0.8857 (mp0)
REVERT: G   28 ILE cc_start: 0.8700 (mm) cc_final: 0.8079 (tp)
REVERT: G   32 LYS cc_start: 0.8679 (tptm) cc_final: 0.8440 (tppp)
REVERT: G   46 LYS cc_start: 0.9037 (pmtt) cc_final: 0.8791 (pmtt)
REVERT: G   48 ASP cc_start: 0.8273 (t0) cc_final: 0.7678 (t0)
REVERT: S   13 GLN cc_start: 0.9173 (tp40) cc_final: 0.8582 (pp30)
REVERT: S   87 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8190 (mtp-110)
REVERT: S   90 ASP cc_start: 0.9211 (m-30) cc_final: 0.8624 (m-30)
REVERT: S   93 MET cc_start: 0.8886 (tpt) cc_final: 0.8451 (tpt)
  outliers start: 27
  outliers final: 11
  residues processed: 187
  average time/residue: 0.6022
  time to fit residues: 119.3986
Evaluate side-chains
  175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  237 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 25 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 86 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.113926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.083169 restraints weight = 18171.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 3.57
r_work: 0.3032 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9018  Z= 0.131
  Angle     :  0.638  10.041  12209  Z= 0.326
  Chirality :  0.044   0.169   1388
  Planarity :  0.004   0.039   1545
  Dihedral  :  4.782  24.168   1231
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.79 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.25), residues: 1115
  helix:  0.55 (0.27), residues: 406
  sheet: -0.53 (0.33), residues: 273
  loop : -1.63 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG S 160 
 TYR   0.013   0.001   TYR R 150 
 PHE   0.020   0.001   PHE A 340 
 TRP   0.012   0.002   TRP B 169 
 HIS   0.006   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9015)
  covalent geometry    : angle       0.63829 (12203)
  SS BOND              : bond        0.00398 (    3)
  SS BOND              : angle       0.83125 (    6)
  hydrogen bonds       : bond        0.03922 (  411)
  hydrogen bonds       : angle       4.73104 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 182
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   53 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7735 (pp20)
REVERT: R   82 ASP cc_start: 0.8118 (t70) cc_final: 0.7749 (t70)
REVERT: R  119 ASP cc_start: 0.7908 (p0) cc_final: 0.7669 (p0)
REVERT: R  149 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7662 (mmm160)
REVERT: R  180 TYR cc_start: 0.7187 (t80) cc_final: 0.6973 (t80)
REVERT: R  193 MET cc_start: 0.8113 (ppp) cc_final: 0.7894 (ppp)
REVERT: R  235 GLN cc_start: 0.8001 (tt0) cc_final: 0.7599 (tt0)
REVERT: R  273 PHE cc_start: 0.9213 (t80) cc_final: 0.8797 (t80)
REVERT: R  274 MET cc_start: 0.8451 (mmm) cc_final: 0.8150 (mmm)
REVERT: R  297 PHE cc_start: 0.7688 (t80) cc_final: 0.7271 (t80)
REVERT: R  301 GLU cc_start: 0.8559 (pm20) cc_final: 0.8249 (pp20)
REVERT: A   61 ARG cc_start: 0.8190 (tpm170) cc_final: 0.7911 (tpm170)
REVERT: A   63 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7439 (p90)
REVERT: A  392 GLU cc_start: 0.8200 (tp30) cc_final: 0.7722 (tp30)
REVERT: B   14 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9167 (mt)
REVERT: B   59 TYR cc_start: 0.8686 (m-80) cc_final: 0.8237 (m-80)
REVERT: B  217 MET cc_start: 0.8690 (pmm) cc_final: 0.8332 (pmm)
REVERT: B  298 ASP cc_start: 0.7911 (t70) cc_final: 0.7635 (t70)
REVERT: G   28 ILE cc_start: 0.8677 (mm) cc_final: 0.8091 (tp)
REVERT: G   32 LYS cc_start: 0.8689 (tptm) cc_final: 0.8467 (tppp)
REVERT: G   46 LYS cc_start: 0.9118 (pmtt) cc_final: 0.8877 (pmtt)
REVERT: G   48 ASP cc_start: 0.8213 (t0) cc_final: 0.7534 (t0)
REVERT: S   13 GLN cc_start: 0.9168 (tp40) cc_final: 0.8607 (pp30)
REVERT: S   90 ASP cc_start: 0.9181 (m-30) cc_final: 0.8624 (m-30)
REVERT: S   93 MET cc_start: 0.8833 (tpt) cc_final: 0.8449 (tpt)
REVERT: S  186 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7297 (tm-30)
REVERT: S  233 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8658 (mm)
  outliers start: 25
  outliers final: 6
  residues processed: 190
  average time/residue: 0.5904
  time to fit residues: 119.0884
Evaluate side-chains
  174 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  234 MET
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
S  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.107830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.076019 restraints weight = 18156.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 3.57
r_work: 0.2904 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061   9018  Z= 0.352
  Angle     :  0.775   9.934  12209  Z= 0.401
  Chirality :  0.048   0.159   1388
  Planarity :  0.005   0.048   1545
  Dihedral  :  5.409  26.336   1231
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 21.98 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.25), residues: 1115
  helix:  0.44 (0.26), residues: 400
  sheet: -0.88 (0.31), residues: 291
  loop : -1.62 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG S 160 
 TYR   0.021   0.002   TYR R 150 
 PHE   0.039   0.002   PHE A 340 
 TRP   0.016   0.002   TRP B  99 
 HIS   0.007   0.002   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00806 ( 9015)
  covalent geometry    : angle       0.77488 (12203)
  SS BOND              : bond        0.00393 (    3)
  SS BOND              : angle       0.83931 (    6)
  hydrogen bonds       : bond        0.04844 (  411)
  hydrogen bonds       : angle       5.10284 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ASP cc_start: 0.8112 (t70) cc_final: 0.7900 (t70)
REVERT: R  193 MET cc_start: 0.8232 (ppp) cc_final: 0.8022 (ppp)
REVERT: R  235 GLN cc_start: 0.8215 (tt0) cc_final: 0.7727 (tt0)
REVERT: R  273 PHE cc_start: 0.9272 (t80) cc_final: 0.8854 (t80)
REVERT: R  274 MET cc_start: 0.8337 (mmm) cc_final: 0.8055 (mmm)
REVERT: R  279 MET cc_start: 0.7999 (pmm) cc_final: 0.6971 (ttt)
REVERT: R  297 PHE cc_start: 0.8010 (t80) cc_final: 0.7478 (OUTLIER)
REVERT: A   27 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8054 (mm-30)
REVERT: A  392 GLU cc_start: 0.8367 (tp30) cc_final: 0.7939 (tp30)
REVERT: B   45 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8306 (mpp)
REVERT: B   57 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8225 (mtpp)
REVERT: B   59 TYR cc_start: 0.8950 (m-80) cc_final: 0.8437 (m-80)
REVERT: B  217 MET cc_start: 0.8525 (pmm) cc_final: 0.8194 (pmm)
REVERT: B  298 ASP cc_start: 0.8201 (t70) cc_final: 0.7841 (t70)
REVERT: B  338 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8722 (mp)
REVERT: G   48 ASP cc_start: 0.8406 (t0) cc_final: 0.7842 (t0)
REVERT: S   13 GLN cc_start: 0.9150 (tp40) cc_final: 0.8364 (pp30)
REVERT: S   83 MET cc_start: 0.9076 (mtm) cc_final: 0.8518 (mtm)
REVERT: S   87 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8234 (mtp-110)
REVERT: S   89 GLU cc_start: 0.8808 (pp20) cc_final: 0.8412 (tm-30)
REVERT: S   90 ASP cc_start: 0.9177 (m-30) cc_final: 0.8590 (m-30)
REVERT: S   93 MET cc_start: 0.8889 (tpt) cc_final: 0.8449 (tpt)
REVERT: S  113 GLN cc_start: 0.8522 (mm110) cc_final: 0.8195 (mt0)
REVERT: S  186 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7463 (tm-30)
  outliers start: 35
  outliers final: 17
  residues processed: 181
  average time/residue: 0.6152
  time to fit residues: 118.1676
Evaluate side-chains
  175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  105 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  237 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 104 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.112260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.081458 restraints weight = 17998.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.55
r_work: 0.3003 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9018  Z= 0.142
  Angle     :  0.677  10.749  12209  Z= 0.346
  Chirality :  0.044   0.186   1388
  Planarity :  0.004   0.051   1545
  Dihedral  :  4.910  23.785   1231
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 22.50 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.25), residues: 1115
  helix:  0.43 (0.26), residues: 406
  sheet: -0.60 (0.32), residues: 284
  loop : -1.61 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG S 160 
 TYR   0.019   0.001   TYR R 150 
 PHE   0.027   0.001   PHE A 340 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9015)
  covalent geometry    : angle       0.67715 (12203)
  SS BOND              : bond        0.00404 (    3)
  SS BOND              : angle       0.75641 (    6)
  hydrogen bonds       : bond        0.03954 (  411)
  hydrogen bonds       : angle       4.79068 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  180 TYR cc_start: 0.7021 (t80) cc_final: 0.6813 (t80)
REVERT: R  213 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7701 (ttp-110)
REVERT: R  235 GLN cc_start: 0.8124 (tt0) cc_final: 0.7435 (tt0)
REVERT: R  273 PHE cc_start: 0.9289 (t80) cc_final: 0.8825 (t80)
REVERT: R  274 MET cc_start: 0.8359 (mmm) cc_final: 0.8065 (mmm)
REVERT: R  279 MET cc_start: 0.7943 (pmm) cc_final: 0.6813 (ttt)
REVERT: R  297 PHE cc_start: 0.7973 (t80) cc_final: 0.7251 (t80)
REVERT: R  301 GLU cc_start: 0.8511 (pm20) cc_final: 0.8186 (pp20)
REVERT: R  303 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7395 (mpp80)
REVERT: A   21 GLU cc_start: 0.7924 (mp0) cc_final: 0.6831 (mp0)
REVERT: A   27 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8029 (mm-30)
REVERT: A   61 ARG cc_start: 0.8291 (tpm170) cc_final: 0.7855 (tpm170)
REVERT: A  318 TYR cc_start: 0.6916 (t80) cc_final: 0.6677 (t80)
REVERT: A  333 ARG cc_start: 0.8574 (tpm170) cc_final: 0.8229 (tpm170)
REVERT: A  392 GLU cc_start: 0.8220 (tp30) cc_final: 0.7695 (tp30)
REVERT: B   57 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8075 (mtpp)
REVERT: B   59 TYR cc_start: 0.8867 (m-80) cc_final: 0.8135 (m-80)
REVERT: B  217 MET cc_start: 0.8605 (pmm) cc_final: 0.8278 (pmm)
REVERT: B  223 THR cc_start: 0.8687 (p) cc_final: 0.8458 (p)
REVERT: B  298 ASP cc_start: 0.7942 (t70) cc_final: 0.7548 (t70)
REVERT: G   20 LYS cc_start: 0.9521 (mtmt) cc_final: 0.9240 (ptpp)
REVERT: G   21 MET cc_start: 0.9230 (mmp) cc_final: 0.8945 (mpm)
REVERT: G   28 ILE cc_start: 0.8753 (mm) cc_final: 0.8090 (tp)
REVERT: G   46 LYS cc_start: 0.9112 (pmtt) cc_final: 0.8830 (pmtt)
REVERT: G   47 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8113 (mm-30)
REVERT: G   48 ASP cc_start: 0.8324 (t0) cc_final: 0.7726 (t0)
REVERT: S   13 GLN cc_start: 0.9104 (tp40) cc_final: 0.8397 (pp30)
REVERT: S   89 GLU cc_start: 0.8849 (pp20) cc_final: 0.8481 (tm-30)
REVERT: S   90 ASP cc_start: 0.9127 (m-30) cc_final: 0.8454 (m-30)
REVERT: S   93 MET cc_start: 0.8848 (tpt) cc_final: 0.8445 (tpt)
REVERT: S  113 GLN cc_start: 0.8534 (mm110) cc_final: 0.8140 (mt0)
REVERT: S  186 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7284 (tm-30)
REVERT: S  212 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.7168 (m-80)
REVERT: S  233 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8719 (mm)
  outliers start: 33
  outliers final: 9
  residues processed: 188
  average time/residue: 0.5837
  time to fit residues: 116.6911
Evaluate side-chains
  179 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  105 VAL
Chi-restraints excluded: chain R residue  213 ARG
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  212 PHE
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  237 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 107 optimal weight:    0.0770
   chunk 10 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0170
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.115068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.084663 restraints weight = 17908.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 3.52
r_work: 0.3065 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9018  Z= 0.123
  Angle     :  0.687  12.661  12209  Z= 0.342
  Chirality :  0.044   0.260   1388
  Planarity :  0.004   0.051   1545
  Dihedral  :  4.640  23.770   1231
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.27 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.26), residues: 1115
  helix:  0.50 (0.27), residues: 403
  sheet: -0.46 (0.32), residues: 285
  loop : -1.49 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG S 160 
 TYR   0.020   0.001   TYR R 150 
 PHE   0.016   0.001   PHE A 340 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9015)
  covalent geometry    : angle       0.68686 (12203)
  SS BOND              : bond        0.00448 (    3)
  SS BOND              : angle       0.74260 (    6)
  hydrogen bonds       : bond        0.03768 (  411)
  hydrogen bonds       : angle       4.62424 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ASP cc_start: 0.8321 (t70) cc_final: 0.8032 (t70)
REVERT: R  235 GLN cc_start: 0.7977 (tt0) cc_final: 0.7306 (tt0)
REVERT: R  273 PHE cc_start: 0.9211 (t80) cc_final: 0.8781 (t80)
REVERT: R  274 MET cc_start: 0.8357 (mmm) cc_final: 0.8058 (mmm)
REVERT: R  279 MET cc_start: 0.7758 (pmm) cc_final: 0.7527 (pmm)
REVERT: R  280 TYR cc_start: 0.7652 (m-10) cc_final: 0.7433 (m-10)
REVERT: R  293 LEU cc_start: 0.9025 (tp) cc_final: 0.8777 (tp)
REVERT: R  297 PHE cc_start: 0.7972 (t80) cc_final: 0.7303 (t80)
REVERT: R  301 GLU cc_start: 0.8462 (pm20) cc_final: 0.7806 (pp20)
REVERT: R  303 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7360 (mpp80)
REVERT: A   27 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7945 (mm-30)
REVERT: A   61 ARG cc_start: 0.8225 (tpm170) cc_final: 0.7792 (tpm170)
REVERT: A  333 ARG cc_start: 0.8481 (tpm170) cc_final: 0.8228 (tpm170)
REVERT: A  378 ASP cc_start: 0.8550 (m-30) cc_final: 0.8332 (m-30)
REVERT: A  392 GLU cc_start: 0.8191 (tp30) cc_final: 0.7665 (tp30)
REVERT: B    9 GLN cc_start: 0.9536 (tp-100) cc_final: 0.9083 (tm-30)
REVERT: B   10 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8524 (pm20)
REVERT: B   57 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8037 (ttmm)
REVERT: B   59 TYR cc_start: 0.8781 (m-80) cc_final: 0.8012 (m-80)
REVERT: B  217 MET cc_start: 0.8634 (pmm) cc_final: 0.8301 (pmm)
REVERT: B  298 ASP cc_start: 0.7942 (t70) cc_final: 0.7569 (t70)
REVERT: B  338 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8631 (mp)
REVERT: B  339 TRP cc_start: 0.8209 (m100) cc_final: 0.7864 (m100)
REVERT: G   17 GLU cc_start: 0.8965 (mp0) cc_final: 0.8716 (pm20)
REVERT: G   20 LYS cc_start: 0.9538 (mtmt) cc_final: 0.9245 (ptpt)
REVERT: G   21 MET cc_start: 0.9240 (mmp) cc_final: 0.8952 (mpm)
REVERT: G   28 ILE cc_start: 0.8691 (mm) cc_final: 0.8104 (tp)
REVERT: G   31 SER cc_start: 0.8517 (t) cc_final: 0.8191 (m)
REVERT: G   46 LYS cc_start: 0.9152 (pmtt) cc_final: 0.8825 (pmtt)
REVERT: G   47 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8198 (mp0)
REVERT: G   48 ASP cc_start: 0.8261 (t0) cc_final: 0.7648 (t0)
REVERT: S   13 GLN cc_start: 0.9080 (tp40) cc_final: 0.8374 (pp30)
REVERT: S   76 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8846 (ptpp)
REVERT: S   89 GLU cc_start: 0.8890 (pp20) cc_final: 0.8466 (tm-30)
REVERT: S   90 ASP cc_start: 0.9023 (m-30) cc_final: 0.8271 (m-30)
REVERT: S   93 MET cc_start: 0.8832 (tpt) cc_final: 0.8449 (tpt)
REVERT: S  113 GLN cc_start: 0.8514 (mm110) cc_final: 0.8251 (mm-40)
REVERT: S  186 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7305 (tm-30)
REVERT: S  212 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7212 (m-80)
REVERT: S  222 GLU cc_start: 0.8926 (pm20) cc_final: 0.8675 (mp0)
REVERT: S  233 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8737 (mm)
  outliers start: 28
  outliers final: 13
  residues processed: 190
  average time/residue: 0.5586
  time to fit residues: 113.0621
Evaluate side-chains
  189 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  105 VAL
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  212 PHE
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  237 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.112495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.081864 restraints weight = 18074.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 3.51
r_work: 0.3007 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9018  Z= 0.167
  Angle     :  0.706  11.706  12209  Z= 0.355
  Chirality :  0.045   0.252   1388
  Planarity :  0.004   0.060   1545
  Dihedral  :  4.748  23.692   1231
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 25.21 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.26), residues: 1115
  helix:  0.53 (0.26), residues: 405
  sheet: -0.45 (0.31), residues: 286
  loop : -1.40 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG S 160 
 TYR   0.019   0.001   TYR R 150 
 PHE   0.018   0.001   PHE A 340 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9015)
  covalent geometry    : angle       0.70622 (12203)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       0.50531 (    6)
  hydrogen bonds       : bond        0.04012 (  411)
  hydrogen bonds       : angle       4.67997 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ASP cc_start: 0.8237 (t70) cc_final: 0.7954 (t70)
REVERT: R  235 GLN cc_start: 0.8013 (tt0) cc_final: 0.7403 (tt0)
REVERT: R  273 PHE cc_start: 0.9245 (t80) cc_final: 0.8821 (t80)
REVERT: R  274 MET cc_start: 0.8298 (mmm) cc_final: 0.7990 (mmm)
REVERT: R  279 MET cc_start: 0.7769 (pmm) cc_final: 0.7536 (pmm)
REVERT: R  280 TYR cc_start: 0.7652 (m-10) cc_final: 0.7424 (m-10)
REVERT: R  293 LEU cc_start: 0.9117 (tp) cc_final: 0.8876 (tp)
REVERT: R  297 PHE cc_start: 0.7998 (t80) cc_final: 0.7360 (t80)
REVERT: R  301 GLU cc_start: 0.8500 (pm20) cc_final: 0.7917 (pp20)
REVERT: A   27 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7947 (mm-30)
REVERT: A  333 ARG cc_start: 0.8486 (tpm170) cc_final: 0.8209 (tpm170)
REVERT: A  378 ASP cc_start: 0.8755 (m-30) cc_final: 0.8537 (m-30)
REVERT: A  392 GLU cc_start: 0.8280 (tp30) cc_final: 0.7774 (tp30)
REVERT: B   57 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8086 (mtpp)
REVERT: B   59 TYR cc_start: 0.8883 (m-80) cc_final: 0.8244 (m-80)
REVERT: B  217 MET cc_start: 0.8603 (pmm) cc_final: 0.8277 (pmm)
REVERT: B  298 ASP cc_start: 0.7991 (t70) cc_final: 0.7556 (t70)
REVERT: B  338 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8645 (mp)
REVERT: G   14 LYS cc_start: 0.9470 (ttpp) cc_final: 0.9228 (ttpp)
REVERT: G   17 GLU cc_start: 0.8949 (mp0) cc_final: 0.8660 (pm20)
REVERT: G   20 LYS cc_start: 0.9542 (mtmt) cc_final: 0.9237 (ptpt)
REVERT: G   21 MET cc_start: 0.9253 (mmp) cc_final: 0.8903 (mpm)
REVERT: G   28 ILE cc_start: 0.8738 (mm) cc_final: 0.8121 (tp)
REVERT: G   31 SER cc_start: 0.8527 (t) cc_final: 0.8207 (m)
REVERT: G   46 LYS cc_start: 0.9148 (pmtt) cc_final: 0.8804 (pmtt)
REVERT: G   47 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8242 (mp0)
REVERT: G   48 ASP cc_start: 0.8331 (t0) cc_final: 0.7739 (t0)
REVERT: S   13 GLN cc_start: 0.9057 (tp40) cc_final: 0.8371 (pp30)
REVERT: S   87 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8230 (mtp-110)
REVERT: S   89 GLU cc_start: 0.8887 (pp20) cc_final: 0.8489 (tm-30)
REVERT: S   90 ASP cc_start: 0.9037 (m-30) cc_final: 0.8377 (m-30)
REVERT: S   93 MET cc_start: 0.8821 (tpt) cc_final: 0.8440 (tpt)
REVERT: S  113 GLN cc_start: 0.8502 (mm110) cc_final: 0.8262 (mm-40)
REVERT: S  186 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7347 (tm-30)
REVERT: S  212 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7297 (m-80)
REVERT: S  222 GLU cc_start: 0.8921 (pm20) cc_final: 0.8697 (mm-30)
REVERT: S  233 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8686 (mm)
REVERT: S  246 GLU cc_start: 0.6835 (mp0) cc_final: 0.6585 (pm20)
  outliers start: 28
  outliers final: 17
  residues processed: 181
  average time/residue: 0.5963
  time to fit residues: 114.6481
Evaluate side-chains
  185 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  105 VAL
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  212 PHE
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  230 MET
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  237 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0570
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0970
   chunk 102 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.115117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.084363 restraints weight = 17883.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 3.53
r_work: 0.3064 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9018  Z= 0.130
  Angle     :  0.716  12.834  12209  Z= 0.357
  Chirality :  0.044   0.207   1388
  Planarity :  0.004   0.061   1545
  Dihedral  :  4.618  23.959   1231
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 26.15 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.26), residues: 1115
  helix:  0.56 (0.26), residues: 403
  sheet: -0.34 (0.31), residues: 291
  loop : -1.33 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG S 160 
 TYR   0.024   0.001   TYR R 150 
 PHE   0.015   0.001   PHE A 340 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.007   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9015)
  covalent geometry    : angle       0.71630 (12203)
  SS BOND              : bond        0.00311 (    3)
  SS BOND              : angle       0.56711 (    6)
  hydrogen bonds       : bond        0.03862 (  411)
  hydrogen bonds       : angle       4.61993 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  121 MET cc_start: 0.7449 (ptm) cc_final: 0.6745 (ppp)
REVERT: R  235 GLN cc_start: 0.7997 (tt0) cc_final: 0.7406 (tt0)
REVERT: R  273 PHE cc_start: 0.9195 (t80) cc_final: 0.8718 (t80)
REVERT: R  274 MET cc_start: 0.8348 (mmm) cc_final: 0.8072 (mmm)
REVERT: R  279 MET cc_start: 0.7732 (pmm) cc_final: 0.7484 (pmm)
REVERT: R  297 PHE cc_start: 0.7988 (t80) cc_final: 0.7056 (t80)
REVERT: R  301 GLU cc_start: 0.8473 (pm20) cc_final: 0.7926 (pp20)
REVERT: R  303 ARG cc_start: 0.7711 (mpp80) cc_final: 0.6886 (mtm-85)
REVERT: A   27 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7938 (mm-30)
REVERT: A   61 ARG cc_start: 0.8148 (tpm170) cc_final: 0.7822 (tpm170)
REVERT: A  333 ARG cc_start: 0.8536 (tpm170) cc_final: 0.8294 (tpm170)
REVERT: A  378 ASP cc_start: 0.8598 (m-30) cc_final: 0.8365 (m-30)
REVERT: A  392 GLU cc_start: 0.8220 (tp30) cc_final: 0.7699 (tp30)
REVERT: B   45 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8229 (mpp)
REVERT: B   57 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8101 (ttmm)
REVERT: B   59 TYR cc_start: 0.8830 (m-80) cc_final: 0.8129 (m-80)
REVERT: B  217 MET cc_start: 0.8609 (pmm) cc_final: 0.8298 (pmm)
REVERT: B  223 THR cc_start: 0.8809 (p) cc_final: 0.8556 (p)
REVERT: B  298 ASP cc_start: 0.7954 (t70) cc_final: 0.7551 (t70)
REVERT: B  338 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8600 (mp)
REVERT: B  339 TRP cc_start: 0.8178 (m100) cc_final: 0.7855 (m100)
REVERT: G   14 LYS cc_start: 0.9477 (ttpp) cc_final: 0.9227 (ttpp)
REVERT: G   17 GLU cc_start: 0.8938 (mp0) cc_final: 0.8686 (pm20)
REVERT: G   20 LYS cc_start: 0.9538 (mtmt) cc_final: 0.9222 (ptpt)
REVERT: G   21 MET cc_start: 0.9232 (mmp) cc_final: 0.8972 (mpm)
REVERT: G   28 ILE cc_start: 0.8715 (mm) cc_final: 0.8142 (OUTLIER)
REVERT: G   31 SER cc_start: 0.8479 (t) cc_final: 0.8161 (m)
REVERT: G   46 LYS cc_start: 0.9168 (pmtt) cc_final: 0.8810 (pmtt)
REVERT: G   47 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8225 (mp0)
REVERT: G   48 ASP cc_start: 0.8271 (t0) cc_final: 0.7662 (t0)
REVERT: S   13 GLN cc_start: 0.9055 (tp40) cc_final: 0.8405 (pp30)
REVERT: S   76 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8796 (ptpp)
REVERT: S   87 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8228 (mtp-110)
REVERT: S   89 GLU cc_start: 0.8908 (pp20) cc_final: 0.8481 (tm-30)
REVERT: S   90 ASP cc_start: 0.9008 (m-30) cc_final: 0.8290 (m-30)
REVERT: S   93 MET cc_start: 0.8839 (tpt) cc_final: 0.8439 (tpt)
REVERT: S  113 GLN cc_start: 0.8492 (mm110) cc_final: 0.8240 (mm-40)
REVERT: S  186 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7298 (tm-30)
REVERT: S  212 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7210 (m-80)
REVERT: S  222 GLU cc_start: 0.8926 (pm20) cc_final: 0.8687 (mm-30)
REVERT: S  230 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7302 (ttp)
REVERT: S  233 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8709 (mm)
REVERT: S  244 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8077 (ttpp)
  outliers start: 21
  outliers final: 14
  residues processed: 188
  average time/residue: 0.5693
  time to fit residues: 114.2125
Evaluate side-chains
  187 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  105 VAL
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  212 PHE
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  230 MET
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  237 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.1980
   chunk 7 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0050
   chunk 17 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 6 optimal weight:   30.0000
   chunk 82 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.114963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.084461 restraints weight = 17952.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 3.51
r_work: 0.3071 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9018  Z= 0.138
  Angle     :  0.727  12.193  12209  Z= 0.364
  Chirality :  0.044   0.252   1388
  Planarity :  0.004   0.065   1545
  Dihedral  :  4.638  25.676   1231
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 26.56 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.26), residues: 1115
  helix:  0.59 (0.27), residues: 396
  sheet: -0.25 (0.32), residues: 292
  loop : -1.30 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG S 160 
 TYR   0.023   0.001   TYR R 150 
 PHE   0.017   0.001   PHE A 340 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9015)
  covalent geometry    : angle       0.72753 (12203)
  SS BOND              : bond        0.00313 (    3)
  SS BOND              : angle       0.55583 (    6)
  hydrogen bonds       : bond        0.03902 (  411)
  hydrogen bonds       : angle       4.60203 ( 1167)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ASP cc_start: 0.7986 (t70) cc_final: 0.7762 (t70)
REVERT: R   83 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (mmp)
REVERT: R  121 MET cc_start: 0.7429 (ptm) cc_final: 0.6719 (ppp)
REVERT: R  235 GLN cc_start: 0.7982 (tt0) cc_final: 0.7462 (tt0)
REVERT: R  273 PHE cc_start: 0.9217 (t80) cc_final: 0.8780 (t80)
REVERT: R  274 MET cc_start: 0.8397 (mmm) cc_final: 0.8095 (mmm)
REVERT: R  279 MET cc_start: 0.7708 (pmm) cc_final: 0.6559 (ttt)
REVERT: R  293 LEU cc_start: 0.9107 (tp) cc_final: 0.8876 (tm)
REVERT: R  297 PHE cc_start: 0.7999 (t80) cc_final: 0.7365 (t80)
REVERT: R  301 GLU cc_start: 0.8456 (pm20) cc_final: 0.7886 (pp20)
REVERT: A   27 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7922 (mm-30)
REVERT: A   61 ARG cc_start: 0.8120 (tpm170) cc_final: 0.7805 (tpm170)
REVERT: A  333 ARG cc_start: 0.8468 (tpm170) cc_final: 0.8198 (tpm170)
REVERT: A  378 ASP cc_start: 0.8631 (m-30) cc_final: 0.8396 (m-30)
REVERT: A  392 GLU cc_start: 0.8212 (tp30) cc_final: 0.7624 (tp30)
REVERT: B    9 GLN cc_start: 0.9555 (tp-100) cc_final: 0.9185 (tm-30)
REVERT: B   10 GLU cc_start: 0.9347 (pm20) cc_final: 0.9091 (pm20)
REVERT: B   45 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8185 (mpp)
REVERT: B   57 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8091 (ttmm)
REVERT: B   59 TYR cc_start: 0.8786 (m-80) cc_final: 0.8050 (m-80)
REVERT: B  217 MET cc_start: 0.8602 (pmm) cc_final: 0.8292 (pmm)
REVERT: B  223 THR cc_start: 0.8809 (p) cc_final: 0.8560 (p)
REVERT: B  298 ASP cc_start: 0.7972 (t70) cc_final: 0.7554 (t70)
REVERT: B  338 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8624 (mp)
REVERT: B  339 TRP cc_start: 0.8224 (m100) cc_final: 0.7892 (m100)
REVERT: G   13 ARG cc_start: 0.9349 (ptp-110) cc_final: 0.9088 (ptp90)
REVERT: G   14 LYS cc_start: 0.9486 (ttpp) cc_final: 0.8939 (mmtt)
REVERT: G   17 GLU cc_start: 0.8946 (mp0) cc_final: 0.8637 (pm20)
REVERT: G   20 LYS cc_start: 0.9531 (mtmt) cc_final: 0.9207 (ptpt)
REVERT: G   21 MET cc_start: 0.9240 (mmp) cc_final: 0.8912 (mpm)
REVERT: G   28 ILE cc_start: 0.8737 (mm) cc_final: 0.8193 (tp)
REVERT: G   31 SER cc_start: 0.8516 (t) cc_final: 0.8247 (m)
REVERT: G   46 LYS cc_start: 0.9153 (pmtt) cc_final: 0.8792 (pmtt)
REVERT: G   47 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8198 (mp0)
REVERT: G   48 ASP cc_start: 0.8268 (t0) cc_final: 0.7663 (t0)
REVERT: S   13 GLN cc_start: 0.9051 (tp40) cc_final: 0.8377 (pp30)
REVERT: S   76 LYS cc_start: 0.9068 (mtmm) cc_final: 0.8711 (pmmt)
REVERT: S   87 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8225 (mtp-110)
REVERT: S   89 GLU cc_start: 0.8914 (pp20) cc_final: 0.8476 (tm-30)
REVERT: S   90 ASP cc_start: 0.8983 (m-30) cc_final: 0.8283 (m-30)
REVERT: S   93 MET cc_start: 0.8826 (tpt) cc_final: 0.8426 (tpt)
REVERT: S  113 GLN cc_start: 0.8493 (mm110) cc_final: 0.8234 (mm-40)
REVERT: S  186 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7282 (tm-30)
REVERT: S  212 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7252 (m-80)
REVERT: S  222 GLU cc_start: 0.8908 (pm20) cc_final: 0.8654 (mm-30)
REVERT: S  233 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8727 (mm)
REVERT: S  244 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8078 (ttpp)
  outliers start: 23
  outliers final: 13
  residues processed: 184
  average time/residue: 0.5594
  time to fit residues: 109.4223
Evaluate side-chains
  188 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 MET
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  105 VAL
Chi-restraints excluded: chain R residue  178 ILE
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue   87 ARG
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  212 PHE
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.114790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.083939 restraints weight = 17713.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 3.53
r_work: 0.3059 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9018  Z= 0.145
  Angle     :  0.739  12.149  12209  Z= 0.367
  Chirality :  0.044   0.182   1388
  Planarity :  0.004   0.065   1545
  Dihedral  :  4.656  25.443   1231
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 26.88 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.25), residues: 1115
  helix:  0.57 (0.26), residues: 402
  sheet: -0.23 (0.32), residues: 287
  loop : -1.33 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG S 160 
 TYR   0.023   0.001   TYR R 150 
 PHE   0.015   0.001   PHE A 340 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.008   0.001   HIS R 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9015)
  covalent geometry    : angle       0.73858 (12203)
  SS BOND              : bond        0.00312 (    3)
  SS BOND              : angle       0.58035 (    6)
  hydrogen bonds       : bond        0.03945 (  411)
  hydrogen bonds       : angle       4.58688 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3389.53 seconds
wall clock time: 58 minutes 36.82 seconds (3516.82 seconds total)