Starting phenix.real_space_refine
on Sun Jun  8 00:51:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w2z_32268/06_2025/7w2z_32268.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w2z_32268/06_2025/7w2z_32268.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w2z_32268/06_2025/7w2z_32268.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w2z_32268/06_2025/7w2z_32268.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w2z_32268/06_2025/7w2z_32268.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w2z_32268/06_2025/7w2z_32268.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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      61      5.16       5
     C    5812      2.51       5
     N    1544      2.21       5
     O    1663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9080
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1691
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 208}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2421
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 418
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1760
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "L"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 10
          Classifications: {'peptide': 2}
          Link IDs: {'TRANS': 1}
    Chain: "L"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 131
          Unusual residues: {'K4Q': 1}
          Classifications: {'peptide': 13, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 11, None: 1}
            Not linked:
              pdbres="K4Q L   3 "
              pdbres="PHE L   4 "
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.45, per 1000 atoms: 0.60
  Number of scatterers: 9080
  At special positions: 0
  Unit cell: (109.512, 119.652, 126.75, 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      61     16.00
     O    1663      8.00
     N    1544      7.00
     C    5812      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 198 " distance=2.05
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      36.2% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.554A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.320A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
    Processing helix  chain 'A' and resid 243 through 256
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.865A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 279 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 4.050A  pdb=" N   ALA A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.524A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 71
      removed outlier: 3.947A  pdb=" N   ALA R  44 " --> pdb=" O   ALA R  40 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL R  56 " --> pdb=" O   ALA R  52 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA R  59 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   THR R  64 " --> pdb=" O   GLY R  60 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET R  65 " --> pdb=" O   ASN R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 75
      removed outlier: 3.586A  pdb=" N   ARG R  75 " --> pdb=" O   ARG R  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 72 through 75'
    Processing helix  chain 'R' and resid 76 through 95
      removed outlier: 3.937A  pdb=" N   PHE R  93 " --> pdb=" O   ASP R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 95 through 105
      removed outlier: 3.510A  pdb=" N   ASP R  99 " --> pdb=" O   CYS R  95 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU R 100 " --> pdb=" O   MET R  96 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 114 through 147
      removed outlier: 3.734A  pdb=" N   LEU R 118 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR R 128 " --> pdb=" O   GLU R 124 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ILE R 145 " --> pdb=" O   ARG R 141 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE R 147 " --> pdb=" O   PHE R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 159 through 175
      removed outlier: 3.632A  pdb=" N   PHE R 165 " --> pdb=" O   LYS R 161 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA R 175 " --> pdb=" O   ALA R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 181
    Processing helix  chain 'R' and resid 201 through 208
    Processing helix  chain 'R' and resid 208 through 218
      removed outlier: 3.673A  pdb=" N   TRP R 215 " --> pdb=" O   THR R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 240
      removed outlier: 3.577A  pdb=" N   LEU R 223 " --> pdb=" O   ILE R 219 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
      removed outlier: 3.592A  pdb=" N   CYS R 227 " --> pdb=" O   LEU R 223 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL R 230 " --> pdb=" O   PHE R 226 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER R 233 " --> pdb=" O   THR R 229 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG R 237 " --> pdb=" O   SER R 233 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 281
      removed outlier: 3.596A  pdb=" N   VAL R 269 " --> pdb=" O   LEU R 265 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE R 272 " --> pdb=" O   VAL R 268 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   CYS R 275 " --> pdb=" O   ALA R 271 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 281 through 289
    Processing helix  chain 'R' and resid 299 through 304
      removed outlier: 3.633A  pdb=" N   TYR R 303 " --> pdb=" O   GLN R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 315
      removed outlier: 3.677A  pdb=" N   VAL R 310 " --> pdb=" O   LEU R 306 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU R 311 " --> pdb=" O   VAL R 307 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 323
      removed outlier: 3.907A  pdb=" N   TYR R 323 " --> pdb=" O   ASN R 319 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 327 through 339
      removed outlier: 3.547A  pdb=" N   ARG R 331 " --> pdb=" O   SER R 327 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL R 332 " --> pdb=" O   LYS R 328 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 22
      removed outlier: 4.085A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.542A  pdb=" N   ALA G  43 " --> pdb=" O   ALA G  39 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.506A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.972A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.725A  pdb=" N   ASP S 211 " --> pdb=" O   GLU S 208 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 208 through 212'
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.595A  pdb=" N   ILE B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'L' and resid 8 through 14
      removed outlier: 3.881A  pdb=" N   VAL L  12 " --> pdb=" O   GLU L   8 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 9.069A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 182 through 185
      removed outlier: 3.647A  pdb=" N   ARG R 199 " --> pdb=" O   GLY R 183 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.811A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.298A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AA7, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.566A  pdb=" N   VAL S 135 " --> pdb=" O   LYS S 232 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.489A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.841A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.817A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.767A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.945A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.683A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.455A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.86

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        1.06 -     1.21: 2
        1.21 -     1.37: 3077
        1.37 -     1.52: 3750
        1.52 -     1.67: 2359
        1.67 -     1.82: 86
  Bond restraints: 9274
  Sorted by residual:
  bond pdb=" C08 K4Q L   3 "
       pdb=" O10 K4Q L   3 "
    ideal  model  delta    sigma   weight residual
    1.335  1.062  0.273 2.00e-02 2.50e+03 1.87e+02
  bond pdb=" C08 K4Q L   3 "
       pdb=" O09 K4Q L   3 "
    ideal  model  delta    sigma   weight residual
    1.204  1.404 -0.200 2.00e-02 2.50e+03 1.00e+02
  bond pdb=" CB  VAL B  71 "
       pdb=" CG2 VAL B  71 "
    ideal  model  delta    sigma   weight residual
    1.521  1.405  0.116 3.30e-02 9.18e+02 1.24e+01
  bond pdb=" C   VAL S  12 "
       pdb=" N   GLN S  13 "
    ideal  model  delta    sigma   weight residual
    1.329  1.384 -0.055 1.60e-02 3.91e+03 1.19e+01
  bond pdb=" C   MET R  96 "
       pdb=" N   PRO R  97 "
    ideal  model  delta    sigma   weight residual
    1.335  1.377 -0.042 1.36e-02 5.41e+03 9.51e+00
  ... (remaining 9269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.82: 12551
        6.82 -    13.64: 15
       13.64 -    20.46: 2
       20.46 -    27.29: 0
       27.29 -    34.11: 2
  Bond angle restraints: 12570
  Sorted by residual:
  angle pdb=" C07 K4Q L   3 "
        pdb=" C08 K4Q L   3 "
        pdb=" O10 K4Q L   3 "
      ideal   model   delta    sigma   weight residual
     118.23   84.12   34.11 3.00e+00 1.11e-01 1.29e+02
  angle pdb=" O09 K4Q L   3 "
        pdb=" C08 K4Q L   3 "
        pdb=" O10 K4Q L   3 "
      ideal   model   delta    sigma   weight residual
     117.69  151.08  -33.39 3.00e+00 1.11e-01 1.24e+02
  angle pdb=" N   VAL R 212 "
        pdb=" CA  VAL R 212 "
        pdb=" C   VAL R 212 "
      ideal   model   delta    sigma   weight residual
     111.00  103.44    7.56 1.09e+00 8.42e-01 4.81e+01
  angle pdb=" N   LYS R 117 "
        pdb=" CA  LYS R 117 "
        pdb=" C   LYS R 117 "
      ideal   model   delta    sigma   weight residual
     111.69  104.40    7.29 1.23e+00 6.61e-01 3.51e+01
  angle pdb=" N   ASN S 182 "
        pdb=" CA  ASN S 182 "
        pdb=" C   ASN S 182 "
      ideal   model   delta    sigma   weight residual
     109.15  117.61   -8.46 1.44e+00 4.82e-01 3.45e+01
  ... (remaining 12565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.02: 5455
       33.02 -    66.05: 127
       66.05 -    99.07: 11
       99.07 -   132.09: 1
      132.09 -   165.11: 2
  Dihedral angle restraints: 5596
    sinusoidal: 2259
      harmonic: 3337
  Sorted by residual:
  dihedral pdb=" CA  LEU A 353 "
           pdb=" C   LEU A 353 "
           pdb=" N   TYR A 354 "
           pdb=" CA  TYR A 354 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.08  -24.92     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" C11 K4Q L   3 "
           pdb=" C08 K4Q L   3 "
           pdb=" O10 K4Q L   3 "
           pdb=" O09 K4Q L   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.48   14.37  165.11     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C04 K4Q L   3 "
           pdb=" C05 K4Q L   3 "
           pdb=" C06 K4Q L   3 "
           pdb=" C07 K4Q L   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     182.71   25.83  156.88     1      3.00e+01 1.11e-03 2.05e+01
  ... (remaining 5593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1285
       0.097 -    0.194: 130
       0.194 -    0.290: 17
       0.290 -    0.387: 2
       0.387 -    0.484: 1
  Chirality restraints: 1435
  Sorted by residual:
  chirality pdb=" CA  MET S 180 "
            pdb=" N   MET S 180 "
            pdb=" C   MET S 180 "
            pdb=" CB  MET S 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.86e+00
  chirality pdb=" CA  LYS A  46 "
            pdb=" N   LYS A  46 "
            pdb=" C   LYS A  46 "
            pdb=" CB  LYS A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" CA  ARG S 179 "
            pdb=" N   ARG S 179 "
            pdb=" C   ARG S 179 "
            pdb=" CB  ARG S 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.46e+00
  ... (remaining 1432 not shown)

  Planarity restraints: 1577
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C07 K4Q L   3 "    0.018 2.00e-02 2.50e+03   1.03e-01 1.07e+02
        pdb=" C08 K4Q L   3 "   -0.173 2.00e-02 2.50e+03
        pdb=" O09 K4Q L   3 "    0.069 2.00e-02 2.50e+03
        pdb=" O10 K4Q L   3 "    0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 107 "   -0.100 5.00e-02 4.00e+02   1.50e-01 3.61e+01
        pdb=" N   PRO R 108 "    0.260 5.00e-02 4.00e+02
        pdb=" CA  PRO R 108 "   -0.089 5.00e-02 4.00e+02
        pdb=" CD  PRO R 108 "   -0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 277 "    0.050 5.00e-02 4.00e+02   7.41e-02 8.79e+00
        pdb=" N   PRO R 278 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO R 278 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO R 278 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1574 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 107
        2.64 -     3.21: 7511
        3.21 -     3.77: 13404
        3.77 -     4.34: 19629
        4.34 -     4.90: 32621
  Nonbonded interactions: 73272
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  43 "
            pdb=" ND2 ASN A  43 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" OD2 ASP R  99 "
            pdb=" OH  TYR R 313 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE2 GLU R 197 "
            pdb=" OG  SER L   6 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.290 3.040
  ... (remaining 73267 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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.800
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  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:14.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
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      :  0.010   0.273   9279  Z= 0.442
  Angle     :  1.135  34.107  12576  Z= 0.608
  Chirality :  0.064   0.484   1435
  Planarity :  0.009   0.150   1577
  Dihedral  : 14.810 165.115   3431
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.62 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.53 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.20), residues: 1132
  helix: -4.36 (0.12), residues: 390
  sheet: -0.81 (0.28), residues: 295
  loop : -2.09 (0.24), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP R 276 
 HIS   0.008   0.002   HIS R 258 
 PHE   0.024   0.003   PHE B 234 
 TYR   0.048   0.003   TYR B 105 
 ARG   0.014   0.001   ARG S  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28360 (  382)
  hydrogen bonds       : angle       9.72698 ( 1104)
  SS BOND              : bond        0.01293 (    3)
  SS BOND              : angle       2.72522 (    6)
  covalent geometry    : bond        0.00943 ( 9274)
  covalent geometry    : angle       1.13344 (12570)
  Misc. bond           : bond        0.10224 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8227 (mtpt)
REVERT: A  209 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7636 (tpp80)
REVERT: A  252 ASP cc_start: 0.7529 (t0) cc_final: 0.7306 (t0)
REVERT: A  271 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7507 (mptp)
REVERT: A  309 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7213 (mt-10)
REVERT: R   65 MET cc_start: 0.6998 (mtp) cc_final: 0.6746 (mtp)
REVERT: R   70 ARG cc_start: 0.6766 (ttt180) cc_final: 0.6444 (ttt90)
REVERT: R  326 MET cc_start: 0.6695 (mmm) cc_final: 0.6355 (mmt)
REVERT: R  328 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7113 (mptp)
REVERT: G   21 MET cc_start: 0.6579 (tpt) cc_final: 0.6049 (pp-130)
REVERT: G   38 MET cc_start: 0.8176 (ttp) cc_final: 0.7920 (ttp)
REVERT: S    3 GLN cc_start: 0.7676 (pt0) cc_final: 0.7438 (pt0)
REVERT: S  147 CYS cc_start: 0.7079 (t) cc_final: 0.6755 (t)
REVERT: B  254 ASP cc_start: 0.8484 (p0) cc_final: 0.8156 (p0)
REVERT: B  258 ASP cc_start: 0.7730 (t0) cc_final: 0.7195 (t70)
  outliers start: 8
  outliers final: 1
  residues processed: 141
  average time/residue: 1.3122
  time to fit residues: 196.5063
Evaluate side-chains
  109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  119 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
A 312 ASN
A 330 ASN
R  79 ASN
R 196 ASN
** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 324 ASN
G  11 GLN
S 130 GLN
B  13 GLN
B  32 GLN
B 155 ASN
B 239 ASN
B 340 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.165463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.130735 restraints weight = 10301.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.00
r_work: 0.3361 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9279  Z= 0.145
  Angle     :  0.600   7.339  12576  Z= 0.320
  Chirality :  0.044   0.234   1435
  Planarity :  0.007   0.138   1577
  Dihedral  :  8.419 110.288   1392
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.74 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 10.92 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.23), residues: 1132
  helix: -1.88 (0.22), residues: 385
  sheet: -0.19 (0.30), residues: 294
  loop : -1.61 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 280 
 PHE   0.022   0.001   PHE R 119 
 TYR   0.021   0.002   TYR A 297 
 ARG   0.007   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04861 (  382)
  hydrogen bonds       : angle       5.07439 ( 1104)
  SS BOND              : bond        0.00503 (    3)
  SS BOND              : angle       2.00671 (    6)
  covalent geometry    : bond        0.00333 ( 9274)
  covalent geometry    : angle       0.59880 (12570)
  Misc. bond           : bond        0.00067 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 1.078 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8166 (tttt) cc_final: 0.7870 (ttmm)
REVERT: A   35 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8080 (mtpt)
REVERT: A  209 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.6379 (ttp-110)
REVERT: A  295 ASN cc_start: 0.7519 (t0) cc_final: 0.6815 (m110)
REVERT: A  309 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7226 (mt-10)
REVERT: R   70 ARG cc_start: 0.6878 (ttt180) cc_final: 0.6317 (ttt90)
REVERT: R  308 SER cc_start: 0.7745 (OUTLIER) cc_final: 0.7379 (m)
REVERT: R  326 MET cc_start: 0.7556 (mmm) cc_final: 0.7133 (mmt)
REVERT: R  328 LYS cc_start: 0.7460 (mmtt) cc_final: 0.7022 (mptp)
REVERT: S   83 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7972 (mtp)
REVERT: B  219 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7096 (mmt90)
REVERT: B  254 ASP cc_start: 0.8804 (p0) cc_final: 0.8586 (p0)
REVERT: B  258 ASP cc_start: 0.7955 (t0) cc_final: 0.7201 (t70)
REVERT: B  260 GLU cc_start: 0.7964 (pt0) cc_final: 0.7190 (tt0)
  outliers start: 30
  outliers final: 12
  residues processed: 140
  average time/residue: 1.3473
  time to fit residues: 201.1968
Evaluate side-chains
  115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    0.4980
   chunk 65 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0000
   chunk 27 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
** G  11 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.168326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133572 restraints weight = 10469.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.00
r_work: 0.3389 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   9279  Z= 0.108
  Angle     :  0.531   6.025  12576  Z= 0.281
  Chirality :  0.042   0.222   1435
  Planarity :  0.005   0.130   1577
  Dihedral  :  7.278  82.419   1390
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.74 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.08 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.24), residues: 1132
  helix: -0.40 (0.26), residues: 388
  sheet: -0.05 (0.30), residues: 292
  loop : -1.31 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 109 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.022   0.001   PHE R 119 
 TYR   0.018   0.001   TYR R 313 
 ARG   0.006   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  382)
  hydrogen bonds       : angle       4.46763 ( 1104)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       2.01810 (    6)
  covalent geometry    : bond        0.00246 ( 9274)
  covalent geometry    : angle       0.52942 (12570)
  Misc. bond           : bond        0.00028 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 1.155 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8131 (tttt) cc_final: 0.7826 (ttmm)
REVERT: A   35 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8012 (mtpt)
REVERT: A   55 ILE cc_start: 0.7339 (mp) cc_final: 0.7125 (mp)
REVERT: A  188 THR cc_start: 0.8437 (m) cc_final: 0.8151 (p)
REVERT: A  209 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.6321 (ttp-110)
REVERT: A  309 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7159 (mt-10)
REVERT: R   70 ARG cc_start: 0.6812 (ttt180) cc_final: 0.6365 (ttt90)
REVERT: R  264 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.6107 (mmm)
REVERT: R  308 SER cc_start: 0.7476 (OUTLIER) cc_final: 0.7055 (m)
REVERT: R  326 MET cc_start: 0.7465 (mmm) cc_final: 0.7046 (mmt)
REVERT: R  328 LYS cc_start: 0.7290 (mmtt) cc_final: 0.6937 (mptp)
REVERT: G   42 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6952 (mp0)
REVERT: S   83 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7819 (mtp)
REVERT: B  219 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7101 (mmt90)
REVERT: B  258 ASP cc_start: 0.7830 (t0) cc_final: 0.7003 (t70)
REVERT: B  260 GLU cc_start: 0.7905 (pt0) cc_final: 0.7554 (tt0)
  outliers start: 24
  outliers final: 5
  residues processed: 130
  average time/residue: 1.2905
  time to fit residues: 179.2152
Evaluate side-chains
  112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 80 optimal weight:    8.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
R 257 ASN
R 302 GLN
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.163683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.126842 restraints weight = 9833.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.10
r_work: 0.3259 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9279  Z= 0.166
  Angle     :  0.588   7.896  12576  Z= 0.308
  Chirality :  0.044   0.210   1435
  Planarity :  0.005   0.126   1577
  Dihedral  :  7.139  72.549   1390
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.83 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.18 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.24), residues: 1132
  helix:  0.07 (0.26), residues: 388
  sheet:  0.09 (0.30), residues: 292
  loop : -1.19 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.026   0.001   PHE R 119 
 TYR   0.016   0.002   TYR R 313 
 ARG   0.004   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  382)
  hydrogen bonds       : angle       4.54610 ( 1104)
  SS BOND              : bond        0.00378 (    3)
  SS BOND              : angle       2.75019 (    6)
  covalent geometry    : bond        0.00400 ( 9274)
  covalent geometry    : angle       0.58477 (12570)
  Misc. bond           : bond        0.00069 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 101
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7762 (mm)
REVERT: A   21 LYS cc_start: 0.8169 (tttt) cc_final: 0.7877 (ttmm)
REVERT: A   35 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8150 (mtpt)
REVERT: A  209 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.6399 (ttp-110)
REVERT: A  248 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7339 (mt)
REVERT: A  309 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7316 (mt-10)
REVERT: R   70 ARG cc_start: 0.6893 (ttt180) cc_final: 0.6380 (ttt90)
REVERT: R  264 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6350 (mmm)
REVERT: R  308 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7346 (m)
REVERT: R  328 LYS cc_start: 0.7457 (mmtt) cc_final: 0.7130 (mptp)
REVERT: G   42 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7059 (mp0)
REVERT: S   83 MET cc_start: 0.8641 (mtp) cc_final: 0.7843 (mtp)
REVERT: B  219 ARG cc_start: 0.7647 (mtm180) cc_final: 0.7143 (mmt90)
REVERT: B  258 ASP cc_start: 0.7823 (t0) cc_final: 0.7186 (t70)
REVERT: B  260 GLU cc_start: 0.8126 (pt0) cc_final: 0.7785 (tt0)
  outliers start: 38
  outliers final: 19
  residues processed: 123
  average time/residue: 1.8142
  time to fit residues: 237.2698
Evaluate side-chains
  117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain R residue  332 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  205 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0970
   chunk 35 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** G  11 GLN ** 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 = 0.3923 r_free = 0.3923 target = 0.167447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.133453 restraints weight = 10428.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.16
r_work: 0.3378 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9279  Z= 0.112
  Angle     :  0.531   7.949  12576  Z= 0.279
  Chirality :  0.042   0.206   1435
  Planarity :  0.005   0.124   1577
  Dihedral  :  6.564  62.572   1390
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.74 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.00 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.25), residues: 1132
  helix:  0.54 (0.27), residues: 389
  sheet:  0.12 (0.30), residues: 287
  loop : -1.02 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.001   PHE R 119 
 TYR   0.015   0.001   TYR A 297 
 ARG   0.003   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  382)
  hydrogen bonds       : angle       4.27374 ( 1104)
  SS BOND              : bond        0.00393 (    3)
  SS BOND              : angle       2.56229 (    6)
  covalent geometry    : bond        0.00259 ( 9274)
  covalent geometry    : angle       0.52834 (12570)
  Misc. bond           : bond        0.00040 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7684 (mm)
REVERT: A   17 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7520 (mttt)
REVERT: A   21 LYS cc_start: 0.8071 (tttt) cc_final: 0.7800 (ttmm)
REVERT: A   35 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8033 (mtpt)
REVERT: A  209 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.6333 (ttp-110)
REVERT: A  309 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7308 (mt-10)
REVERT: R   70 ARG cc_start: 0.6807 (ttt180) cc_final: 0.6481 (ttt90)
REVERT: R  264 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6194 (mmm)
REVERT: R  308 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.6947 (m)
REVERT: R  328 LYS cc_start: 0.7290 (mmtt) cc_final: 0.6786 (mptp)
REVERT: G   42 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7060 (mp0)
REVERT: S   83 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7870 (mtp)
REVERT: B  258 ASP cc_start: 0.7695 (t0) cc_final: 0.7120 (t70)
REVERT: B  260 GLU cc_start: 0.8020 (pt0) cc_final: 0.7583 (tt0)
  outliers start: 38
  outliers final: 17
  residues processed: 126
  average time/residue: 1.1601
  time to fit residues: 156.8750
Evaluate side-chains
  116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 98 optimal weight:    0.3980
   chunk 95 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0970
   chunk 79 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** G  11 GLN ** 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 = 0.3938 r_free = 0.3938 target = 0.168895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134605 restraints weight = 10405.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.03
r_work: 0.3405 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053   9279  Z= 0.101
  Angle     :  0.514   8.218  12576  Z= 0.270
  Chirality :  0.042   0.200   1435
  Planarity :  0.005   0.123   1577
  Dihedral  :  6.312  59.299   1390
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.83 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.71 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.25), residues: 1132
  helix:  0.81 (0.27), residues: 389
  sheet:  0.17 (0.30), residues: 289
  loop : -0.86 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 109 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.020   0.001   PHE R 119 
 TYR   0.015   0.001   TYR A 297 
 ARG   0.004   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03174 (  382)
  hydrogen bonds       : angle       4.12558 ( 1104)
  SS BOND              : bond        0.00388 (    3)
  SS BOND              : angle       2.42486 (    6)
  covalent geometry    : bond        0.00231 ( 9274)
  covalent geometry    : angle       0.51144 (12570)
  Misc. bond           : bond        0.00021 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7684 (mm)
REVERT: A   17 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7474 (mttt)
REVERT: A   21 LYS cc_start: 0.8047 (tttt) cc_final: 0.7799 (ttmm)
REVERT: A   35 LYS cc_start: 0.8496 (mtmm) cc_final: 0.7981 (mtpt)
REVERT: A  209 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.6316 (ttp-110)
REVERT: A  248 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7288 (mt)
REVERT: A  296 THR cc_start: 0.7524 (OUTLIER) cc_final: 0.6846 (p)
REVERT: A  309 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7350 (mt-10)
REVERT: R   70 ARG cc_start: 0.6786 (ttt180) cc_final: 0.6485 (ttt90)
REVERT: R  264 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6138 (mmm)
REVERT: R  308 SER cc_start: 0.7341 (OUTLIER) cc_final: 0.6814 (m)
REVERT: R  328 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6778 (mptp)
REVERT: G   42 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7201 (mp0)
REVERT: S   83 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7879 (mtp)
REVERT: B  258 ASP cc_start: 0.7717 (t0) cc_final: 0.7149 (t70)
REVERT: B  260 GLU cc_start: 0.7938 (pt0) cc_final: 0.7473 (tt0)
  outliers start: 34
  outliers final: 15
  residues processed: 122
  average time/residue: 1.3804
  time to fit residues: 180.2331
Evaluate side-chains
  113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  308 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    0.1980
   chunk 17 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0770
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.6140

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
R 280 HIS
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.170040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.133606 restraints weight = 9910.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.06
r_work: 0.3330 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9279  Z= 0.091
  Angle     :  0.530  21.937  12576  Z= 0.262
  Chirality :  0.041   0.265   1435
  Planarity :  0.006   0.187   1577
  Dihedral  :  5.998  56.406   1390
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.56 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.02 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1132
  helix:  0.96 (0.27), residues: 396
  sheet:  0.27 (0.30), residues: 287
  loop : -0.77 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 119 
 TYR   0.015   0.001   TYR A 297 
 ARG   0.005   0.000   ARG R 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02965 (  382)
  hydrogen bonds       : angle       3.98496 ( 1104)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       1.97691 (    6)
  covalent geometry    : bond        0.00199 ( 9274)
  covalent geometry    : angle       0.52854 (12570)
  Misc. bond           : bond        0.00015 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 1.275 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8090 (tttt) cc_final: 0.7872 (ttmm)
REVERT: A   35 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8016 (mtpt)
REVERT: A  209 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6327 (ttp-110)
REVERT: A  244 MET cc_start: 0.7388 (tpp) cc_final: 0.7060 (tpp)
REVERT: A  248 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7368 (mt)
REVERT: A  296 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7064 (p)
REVERT: R   70 ARG cc_start: 0.6929 (ttt180) cc_final: 0.6635 (ttt90)
REVERT: R  180 VAL cc_start: 0.6515 (t) cc_final: 0.6243 (m)
REVERT: R  198 CYS cc_start: 0.4135 (OUTLIER) cc_final: 0.3450 (t)
REVERT: R  213 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5930 (tpp)
REVERT: R  264 MET cc_start: 0.6488 (mmm) cc_final: 0.6239 (mmm)
REVERT: R  328 LYS cc_start: 0.7406 (mmtt) cc_final: 0.6928 (mptp)
REVERT: G   42 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7272 (mp0)
REVERT: S   83 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7946 (mtp)
REVERT: B  258 ASP cc_start: 0.7865 (t0) cc_final: 0.7262 (t70)
REVERT: B  260 GLU cc_start: 0.7821 (pt0) cc_final: 0.7432 (tt0)
  outliers start: 30
  outliers final: 14
  residues processed: 121
  average time/residue: 1.1609
  time to fit residues: 151.1585
Evaluate side-chains
  115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0170
   chunk 62 optimal weight:    0.0670
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 110 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.0160

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

Flipped N/Q/H residues before XYZ refinement:
** G  11 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.169360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.135104 restraints weight = 10629.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.03
r_work: 0.3399 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9279  Z= 0.105
  Angle     :  0.530  15.468  12576  Z= 0.270
  Chirality :  0.042   0.228   1435
  Planarity :  0.005   0.163   1577
  Dihedral  :  6.035  55.290   1390
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.74 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.43 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1132
  helix:  1.03 (0.27), residues: 395
  sheet:  0.31 (0.30), residues: 287
  loop : -0.77 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.011   0.001   PHE R 119 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.003   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03193 (  382)
  hydrogen bonds       : angle       4.01315 ( 1104)
  SS BOND              : bond        0.00436 (    3)
  SS BOND              : angle       1.89270 (    6)
  covalent geometry    : bond        0.00239 ( 9274)
  covalent geometry    : angle       0.52870 (12570)
  Misc. bond           : bond        0.00022 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 2.626 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7684 (mm)
REVERT: A   17 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7484 (mttt)
REVERT: A   35 LYS cc_start: 0.8459 (mtmm) cc_final: 0.7959 (mtpt)
REVERT: A  209 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.6263 (ttp-110)
REVERT: A  244 MET cc_start: 0.7378 (tpp) cc_final: 0.7062 (tpp)
REVERT: A  248 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7283 (mt)
REVERT: A  296 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.6675 (p)
REVERT: R   70 ARG cc_start: 0.6801 (ttt180) cc_final: 0.6509 (ttt90)
REVERT: R   82 LEU cc_start: 0.8076 (mt) cc_final: 0.7793 (mm)
REVERT: R  180 VAL cc_start: 0.6426 (t) cc_final: 0.6165 (m)
REVERT: R  198 CYS cc_start: 0.4308 (OUTLIER) cc_final: 0.3734 (t)
REVERT: R  213 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5792 (tpp)
REVERT: R  240 TRP cc_start: 0.6347 (OUTLIER) cc_final: 0.5879 (t60)
REVERT: R  264 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.6231 (mmm)
REVERT: R  328 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6816 (mptp)
REVERT: G   42 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7287 (mp0)
REVERT: S   83 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7912 (mtp)
REVERT: B  258 ASP cc_start: 0.7729 (t0) cc_final: 0.7149 (t70)
REVERT: B  260 GLU cc_start: 0.7904 (pt0) cc_final: 0.7467 (tt0)
REVERT: B  262 MET cc_start: 0.8736 (mmt) cc_final: 0.8529 (mmt)
  outliers start: 30
  outliers final: 12
  residues processed: 114
  average time/residue: 1.2725
  time to fit residues: 155.6347
Evaluate side-chains
  115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  240 TRP
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** G  11 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.169363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.135065 restraints weight = 10401.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.02
r_work: 0.3415 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9279  Z= 0.103
  Angle     :  0.507   6.862  12576  Z= 0.264
  Chirality :  0.041   0.139   1435
  Planarity :  0.004   0.061   1577
  Dihedral  :  6.063  55.722   1390
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.73 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.25), residues: 1132
  helix:  1.06 (0.27), residues: 398
  sheet:  0.31 (0.30), residues: 295
  loop : -0.71 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.012   0.001   PHE R 119 
 TYR   0.017   0.001   TYR R 128 
 ARG   0.008   0.000   ARG R 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03104 (  382)
  hydrogen bonds       : angle       4.00890 ( 1104)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       2.07630 (    6)
  covalent geometry    : bond        0.00235 ( 9274)
  covalent geometry    : angle       0.50486 (12570)
  Misc. bond           : bond        0.00022 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.980 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7467 (mttt)
REVERT: A   35 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7942 (mtpt)
REVERT: A  209 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.6127 (ttp-110)
REVERT: A  244 MET cc_start: 0.7366 (tpp) cc_final: 0.7099 (tpp)
REVERT: A  248 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7274 (mt)
REVERT: A  296 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6638 (p)
REVERT: R   70 ARG cc_start: 0.6770 (ttt180) cc_final: 0.6550 (ttt90)
REVERT: R   82 LEU cc_start: 0.8055 (mt) cc_final: 0.7786 (mm)
REVERT: R  180 VAL cc_start: 0.6414 (t) cc_final: 0.6213 (m)
REVERT: R  198 CYS cc_start: 0.4519 (OUTLIER) cc_final: 0.3602 (t)
REVERT: R  213 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.5780 (tpp)
REVERT: R  240 TRP cc_start: 0.6339 (OUTLIER) cc_final: 0.5930 (t60)
REVERT: R  264 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6210 (mmm)
REVERT: R  328 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6828 (mptp)
REVERT: G   42 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7267 (mp0)
REVERT: S   67 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.5395 (ptm-80)
REVERT: S   83 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7915 (mtp)
REVERT: B  258 ASP cc_start: 0.7733 (t0) cc_final: 0.7138 (t70)
REVERT: B  260 GLU cc_start: 0.7882 (pt0) cc_final: 0.7430 (tt0)
REVERT: B  280 LYS cc_start: 0.8568 (tttm) cc_final: 0.8336 (tttp)
  outliers start: 31
  outliers final: 16
  residues processed: 119
  average time/residue: 1.3234
  time to fit residues: 169.0201
Evaluate side-chains
  121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  156 THR
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  240 TRP
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 87 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0670
   chunk 112 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 52 optimal weight:    9.9990
   chunk 101 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    2.3724

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
R 280 HIS
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.164766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.130380 restraints weight = 10543.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.04
r_work: 0.3350 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9279  Z= 0.179
  Angle     :  0.599   8.517  12576  Z= 0.312
  Chirality :  0.045   0.151   1435
  Planarity :  0.004   0.071   1577
  Dihedral  :  6.730  55.358   1390
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.53 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.25), residues: 1132
  helix:  0.67 (0.27), residues: 398
  sheet:  0.25 (0.30), residues: 293
  loop : -0.74 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.007   0.001   HIS S  35 
 PHE   0.022   0.002   PHE R 119 
 TYR   0.019   0.002   TYR S 178 
 ARG   0.003   0.000   ARG L  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  382)
  hydrogen bonds       : angle       4.37983 ( 1104)
  SS BOND              : bond        0.00590 (    3)
  SS BOND              : angle       2.60395 (    6)
  covalent geometry    : bond        0.00432 ( 9274)
  covalent geometry    : angle       0.59640 (12570)
  Misc. bond           : bond        0.00052 (    2)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7796 (mm)
REVERT: A   17 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7565 (mttt)
REVERT: A   35 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8026 (mtpt)
REVERT: A  209 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.6184 (ttp-110)
REVERT: A  244 MET cc_start: 0.7380 (tpp) cc_final: 0.7159 (tpp)
REVERT: A  296 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.6991 (p)
REVERT: R   70 ARG cc_start: 0.6743 (ttt180) cc_final: 0.6263 (ttt90)
REVERT: R  213 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5846 (tpp)
REVERT: R  240 TRP cc_start: 0.6283 (OUTLIER) cc_final: 0.5820 (t60)
REVERT: R  264 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6258 (mmm)
REVERT: R  328 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6980 (mptp)
REVERT: G   42 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7190 (mp0)
REVERT: S   67 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.5430 (ptm-80)
REVERT: S   83 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7953 (mtp)
REVERT: B  258 ASP cc_start: 0.7899 (t0) cc_final: 0.7123 (t70)
REVERT: B  260 GLU cc_start: 0.8129 (pt0) cc_final: 0.7728 (tt0)
  outliers start: 31
  outliers final: 14
  residues processed: 114
  average time/residue: 1.2682
  time to fit residues: 154.2609
Evaluate side-chains
  110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue  173 CYS
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  240 TRP
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0370
   chunk 110 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0470
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
R 280 HIS
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.169600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135268 restraints weight = 10493.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.02
r_work: 0.3418 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9279  Z= 0.097
  Angle     :  0.513   7.016  12576  Z= 0.267
  Chirality :  0.041   0.148   1435
  Planarity :  0.004   0.064   1577
  Dihedral  :  6.116  57.394   1390
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.96 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.25), residues: 1132
  helix:  1.10 (0.27), residues: 391
  sheet:  0.44 (0.30), residues: 286
  loop : -0.75 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 109 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.024   0.001   PHE R 119 
 TYR   0.022   0.001   TYR R 128 
 ARG   0.002   0.000   ARG S  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02992 (  382)
  hydrogen bonds       : angle       4.01660 ( 1104)
  SS BOND              : bond        0.00365 (    3)
  SS BOND              : angle       2.69299 (    6)
  covalent geometry    : bond        0.00218 ( 9274)
  covalent geometry    : angle       0.50943 (12570)
  Misc. bond           : bond        0.00023 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8238.67 seconds
wall clock time: 146 minutes 55.24 seconds (8815.24 seconds total)