Starting phenix.real_space_refine
on Sun May 11 18:04:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wc4_37430/05_2025/8wc4_37430_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wc4_37430/05_2025/8wc4_37430.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wc4_37430/05_2025/8wc4_37430.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wc4_37430/05_2025/8wc4_37430.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wc4_37430/05_2025/8wc4_37430_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wc4_37430/05_2025/8wc4_37430_neut.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Br      1      7.06       5
     S      56      5.16       5
     C    5369      2.51       5
     N    1426      2.21       5
     O    1542      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8394
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1844
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 5, 'TRANS': 227}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 67
    Chain: "B"
      Number of atoms: 2484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2484
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 104
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "R"
      Number of atoms: 2054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2054
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 12, 'TRANS': 260}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 130
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 55
    Chain: "S"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1622
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 9, 'TRANS': 204}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "Y"
      Number of atoms: 380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 380
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'VMT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.54, per 1000 atoms: 0.66
  Number of scatterers: 8394
  At special positions: 0
  Unit cell: (89.25, 118.15, 124.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Br      1     34.99
     S      56     16.00
     O    1542      8.00
     N    1426      7.00
     C    5369      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " 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=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      38.3% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.680A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.539A  pdb=" N   ARG A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.844A  pdb=" N   GLN A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
      removed outlier: 3.676A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
      removed outlier: 3.729A  pdb=" N   LEU A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
      removed outlier: 3.596A  pdb=" N   TYR A 285 " --> pdb=" O   PHE A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 317
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 7 through 24
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.639A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 25 through 49
      removed outlier: 3.721A  pdb=" N   ILE R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL R  43 " --> pdb=" O   GLY R  39 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE R  44 " --> pdb=" O   ASN R  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 57 through 85
      removed outlier: 4.223A  pdb=" N   LEU R  61 " --> pdb=" O   THR R  57 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   MET R  76 " --> pdb=" O   GLY R  72 " (cutoff:3.500A)
      Proline residue:  R  77  - end of helix
    Processing helix  chain 'R' and resid 94 through 126
      removed outlier: 3.731A  pdb=" N   ALA R 123 " --> pdb=" O   ASP R 119 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   VAL R 124 " --> pdb=" O   ARG R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 134
    Processing helix  chain 'R' and resid 135 through 160
      removed outlier: 3.573A  pdb=" N   ILE R 139 " --> pdb=" O   ASN R 135 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU R 140 " --> pdb=" O   ILE R 136 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   VAL R 141 " --> pdb=" O   SER R 137 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET R 142 " --> pdb=" O   THR R 138 " (cutoff:3.500A)
      Proline residue:  R 150  - end of helix
    Processing helix  chain 'R' and resid 167 through 175
    Processing helix  chain 'R' and resid 188 through 198
    Processing helix  chain 'R' and resid 198 through 226
      removed outlier: 3.538A  pdb=" N   ILE R 223 " --> pdb=" O   GLN R 219 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN R 224 " --> pdb=" O   ALA R 220 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 275
      removed outlier: 3.587A  pdb=" N   THR R 249 " --> pdb=" O   LYS R 245 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
      Proline residue:  R 272  - end of helix
    Processing helix  chain 'R' and resid 279 through 302
      removed outlier: 4.043A  pdb=" N   ASN R 283 " --> pdb=" O   PRO R 279 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASP R 284 " --> pdb=" O   PRO R 280 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA R 285 " --> pdb=" O   SER R 281 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY R 290 " --> pdb=" O   LEU R 286 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   TYR R 291 " --> pdb=" O   TYR R 287 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 305 through 313
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.666A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.903A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 9 through 24
      removed outlier: 3.654A  pdb=" N   ASN Y  24 " --> pdb=" O   LYS Y  20 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 29 through 45
      removed outlier: 3.604A  pdb=" N   ASP Y  36 " --> pdb=" O   LYS Y  32 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU Y  37 " --> pdb=" O   ALA Y  33 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 46 through 48
      No H-bonds generated for 'chain 'Y' and resid 46 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190
      removed outlier: 3.541A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 9.846A  pdb=" N   ALA A 220 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.941A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.728A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.042A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.902A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.574A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.564A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.571A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.608A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 4
      removed outlier: 3.693A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER S  25 " --> pdb=" O   GLN S   3 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG S  18 " --> pdb=" O   MET S  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.658A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142
      removed outlier: 3.566A  pdb=" N   ARG S 160 " --> pdb=" O   THR S 141 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.445A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR S 227 " --> pdb=" O   THR S 243 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.577A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1077 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: 2.40

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        1.16 -     1.31: 1357
        1.31 -     1.47: 3583
        1.47 -     1.63: 3558
        1.63 -     1.78: 7
        1.78 -     1.94: 75
  Bond restraints: 8580
  Sorted by residual:
  bond pdb=" C   PRO R  56 "
       pdb=" O   PRO R  56 "
    ideal  model  delta    sigma   weight residual
    1.238  1.158  0.080 1.24e-02 6.50e+03 4.16e+01
  bond pdb=" C   MET R 195 "
       pdb=" O   MET R 195 "
    ideal  model  delta    sigma   weight residual
    1.236  1.177  0.059 1.16e-02 7.43e+03 2.59e+01
  bond pdb=" CA  ASN A 231 "
       pdb=" C   ASN A 231 "
    ideal  model  delta    sigma   weight residual
    1.525  1.474  0.051 1.02e-02 9.61e+03 2.49e+01
  bond pdb=" C   ASP B 312 "
       pdb=" O   ASP B 312 "
    ideal  model  delta    sigma   weight residual
    1.236  1.167  0.069 1.38e-02 5.25e+03 2.46e+01
  bond pdb=" CA  PHE R  50 "
       pdb=" C   PHE R  50 "
    ideal  model  delta    sigma   weight residual
    1.524  1.490  0.034 7.00e-03 2.04e+04 2.41e+01
  ... (remaining 8575 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 11535
        3.09 -     6.18: 112
        6.18 -     9.27: 16
        9.27 -    12.36: 2
       12.36 -    15.44: 1
  Bond angle restraints: 11666
  Sorted by residual:
  angle pdb=" N   GLN R  52 "
        pdb=" CA  GLN R  52 "
        pdb=" C   GLN R  52 "
      ideal   model   delta    sigma   weight residual
     112.45   97.01   15.44 1.39e+00 5.18e-01 1.23e+02
  angle pdb=" C   ILE R 223 "
        pdb=" CA  ILE R 223 "
        pdb=" CB  ILE R 223 "
      ideal   model   delta    sigma   weight residual
     111.70  102.14    9.56 1.28e+00 6.10e-01 5.58e+01
  angle pdb=" N   ALA R 311 "
        pdb=" CA  ALA R 311 "
        pdb=" C   ALA R 311 "
      ideal   model   delta    sigma   weight residual
     112.90  103.86    9.04 1.31e+00 5.83e-01 4.76e+01
  angle pdb=" C   THR R  55 "
        pdb=" N   PRO R  56 "
        pdb=" CA  PRO R  56 "
      ideal   model   delta    sigma   weight residual
     119.28  126.65   -7.37 1.10e+00 8.26e-01 4.49e+01
  angle pdb=" N   TYR R 305 "
        pdb=" CA  TYR R 305 "
        pdb=" C   TYR R 305 "
      ideal   model   delta    sigma   weight residual
     109.72  117.84   -8.12 1.25e+00 6.40e-01 4.22e+01
  ... (remaining 11661 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 4569
       16.03 -    32.05: 349
       32.05 -    48.08: 75
       48.08 -    64.11: 12
       64.11 -    80.13: 14
  Dihedral angle restraints: 5019
    sinusoidal: 1794
      harmonic: 3225
  Sorted by residual:
  dihedral pdb=" N   LYS R  51 "
           pdb=" C   LYS R  51 "
           pdb=" CA  LYS R  51 "
           pdb=" CB  LYS R  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.77  -16.97     0      2.50e+00 1.60e-01 4.61e+01
  dihedral pdb=" C   LYS R  51 "
           pdb=" N   LYS R  51 "
           pdb=" CA  LYS R  51 "
           pdb=" CB  LYS R  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.57   13.97     0      2.50e+00 1.60e-01 3.12e+01
  dihedral pdb=" C   ILE R  45 "
           pdb=" N   ILE R  45 "
           pdb=" CA  ILE R  45 "
           pdb=" CB  ILE R  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.17   12.17     0      2.50e+00 1.60e-01 2.37e+01
  ... (remaining 5016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1293
       0.120 -    0.239: 39
       0.239 -    0.359: 5
       0.359 -    0.478: 3
       0.478 -    0.598: 1
  Chirality restraints: 1341
  Sorted by residual:
  chirality pdb=" CA  LYS R  51 "
            pdb=" N   LYS R  51 "
            pdb=" C   LYS R  51 "
            pdb=" CB  LYS R  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.94e+00
  chirality pdb=" CA  PHE R  50 "
            pdb=" N   PHE R  50 "
            pdb=" C   PHE R  50 "
            pdb=" CB  PHE R  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" CB  ILE R  45 "
            pdb=" CA  ILE R  45 "
            pdb=" CG1 ILE R  45 "
            pdb=" CG2 ILE R  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.61e+00
  ... (remaining 1338 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R  88 "    0.022 2.00e-02 2.50e+03   4.57e-02 2.09e+01
        pdb=" C   TRP R  88 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   TRP R  88 "    0.030 2.00e-02 2.50e+03
        pdb=" N   TYR R  89 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 194 "   -0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   PHE R 194 "    0.071 2.00e-02 2.50e+03
        pdb=" O   PHE R 194 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   MET R 195 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R  55 "    0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   THR R  55 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   THR R  55 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PRO R  56 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1141
        2.75 -     3.29: 7801
        3.29 -     3.83: 12896
        3.83 -     4.36: 14793
        4.36 -     4.90: 27137
  Nonbonded interactions: 63768
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN R  40 "
            pdb=" OD1 ASP R  68 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O   GLN S  39 "
            pdb=" OG1 THR S 116 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   TYR B  85 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" ND1 HIS B 311 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.334 3.120
  ... (remaining 63763 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:             0.850
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.970
  Find NCS groups from input model:        0.100
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
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      :  0.006   0.080   8582  Z= 0.366
  Angle     :  0.808  15.445  11670  Z= 0.487
  Chirality :  0.059   0.598   1341
  Planarity :  0.005   0.047   1474
  Dihedral  : 13.024  80.132   2927
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  1.28 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.26), residues: 1084
  helix:  1.22 (0.27), residues: 377
  sheet:  0.20 (0.33), residues: 256
  loop : -1.62 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.012   0.002   HIS R  49 
 PHE   0.018   0.002   PHE R 214 
 TYR   0.030   0.002   TYR A 230 
 ARG   0.006   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20606 (  376)
  hydrogen bonds       : angle       6.69945 ( 1077)
  SS BOND              : bond        0.00686 (    2)
  SS BOND              : angle       1.48953 (    4)
  covalent geometry    : bond        0.00588 ( 8580)
  covalent geometry    : angle       0.80814 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 161
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  234 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7431 (tp-100)
REVERT: A  238 ASN cc_start: 0.8730 (m110) cc_final: 0.8403 (m110)
REVERT: A  323 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7818 (ttm110)
REVERT: B  247 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0)
REVERT: R  157 MET cc_start: 0.7804 (ttm) cc_final: 0.7443 (ttm)
REVERT: R  224 ASN cc_start: 0.7546 (m-40) cc_final: 0.7288 (m110)
REVERT: S   18 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7818 (ttm170)
  outliers start: 8
  outliers final: 5
  residues processed: 167
  average time/residue: 0.2333
  time to fit residues: 51.2828
Evaluate side-chains
  135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 HIS
Chi-restraints excluded: chain R residue   54 HIS
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  310 ARG
Chi-restraints excluded: chain Y residue   28 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 204 GLN
B  32 GLN
R  52 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.148854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.113817 restraints weight = 10906.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.52
r_work: 0.3151 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8582  Z= 0.137
  Angle     :  0.590  10.165  11670  Z= 0.311
  Chirality :  0.044   0.145   1341
  Planarity :  0.004   0.042   1474
  Dihedral  :  5.874  59.781   1203
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  6.99 %
    Favored  : 91.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.25), residues: 1084
  helix:  1.85 (0.27), residues: 374
  sheet:  0.31 (0.34), residues: 249
  loop : -1.51 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R  62 
 PHE   0.019   0.001   PHE A 189 
 TYR   0.039   0.002   TYR R 287 
 ARG   0.004   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05777 (  376)
  hydrogen bonds       : angle       4.79973 ( 1077)
  SS BOND              : bond        0.00721 (    2)
  SS BOND              : angle       1.15425 (    4)
  covalent geometry    : bond        0.00303 ( 8580)
  covalent geometry    : angle       0.58931 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8115 (tt0) cc_final: 0.7820 (mt0)
REVERT: A  204 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8236 (mm110)
REVERT: A  238 ASN cc_start: 0.8906 (m110) cc_final: 0.8655 (m110)
REVERT: B  247 ASP cc_start: 0.8055 (t0) cc_final: 0.7802 (t0)
REVERT: R  157 MET cc_start: 0.7913 (ttm) cc_final: 0.7460 (ttm)
REVERT: R  270 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7767 (mm)
REVERT: S   18 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8321 (tpp-160)
REVERT: Y   48 ASP cc_start: 0.8692 (t0) cc_final: 0.8447 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 147
  average time/residue: 0.2245
  time to fit residues: 44.0956
Evaluate side-chains
  132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 HIS
Chi-restraints excluded: chain R residue   54 HIS
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  125 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  270 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 25 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 88 optimal weight:    0.1980
   chunk 92 optimal weight:    3.9990
   chunk 70 optimal weight:   20.0000
   chunk 105 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
B  32 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.144715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111435 restraints weight = 10793.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.31
r_work: 0.3108 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8582  Z= 0.218
  Angle     :  0.651  12.702  11670  Z= 0.339
  Chirality :  0.046   0.157   1341
  Planarity :  0.004   0.043   1474
  Dihedral  :  5.603  55.399   1197
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.42 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.25), residues: 1084
  helix:  1.96 (0.27), residues: 375
  sheet:  0.28 (0.34), residues: 248
  loop : -1.50 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 339 
 HIS   0.010   0.002   HIS R  62 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.029   0.002   TYR R 287 
 ARG   0.006   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06622 (  376)
  hydrogen bonds       : angle       4.74034 ( 1077)
  SS BOND              : bond        0.01010 (    2)
  SS BOND              : angle       1.52704 (    4)
  covalent geometry    : bond        0.00527 ( 8580)
  covalent geometry    : angle       0.65027 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8257 (tt0) cc_final: 0.7990 (mt0)
REVERT: A  204 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8171 (mm110)
REVERT: A  234 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7832 (tp-100)
REVERT: A  238 ASN cc_start: 0.8958 (m110) cc_final: 0.8700 (m110)
REVERT: B   75 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8284 (tt0)
REVERT: R   54 HIS cc_start: 0.6980 (m170) cc_final: 0.6734 (m170)
REVERT: R  157 MET cc_start: 0.8002 (ttm) cc_final: 0.7553 (ttm)
  outliers start: 16
  outliers final: 12
  residues processed: 143
  average time/residue: 0.2138
  time to fit residues: 41.1643
Evaluate side-chains
  138 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   49 HIS
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  100 SER
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  268 THR
Chi-restraints excluded: chain S residue   62 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0870
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 97 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   chunk 15 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 261 GLN
B  32 GLN
R  40 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.149214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.115996 restraints weight = 10741.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.33
r_work: 0.3175 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8582  Z= 0.112
  Angle     :  0.532  11.814  11670  Z= 0.278
  Chirality :  0.042   0.143   1341
  Planarity :  0.004   0.039   1474
  Dihedral  :  4.676  51.550   1193
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.75 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.26), residues: 1084
  helix:  2.31 (0.27), residues: 368
  sheet:  0.43 (0.33), residues: 265
  loop : -1.49 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.009   0.001   HIS R  62 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.019   0.001   TYR A 230 
 ARG   0.008   0.001   ARG A 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04718 (  376)
  hydrogen bonds       : angle       4.39754 ( 1077)
  SS BOND              : bond        0.00577 (    2)
  SS BOND              : angle       0.81566 (    4)
  covalent geometry    : bond        0.00236 ( 8580)
  covalent geometry    : angle       0.53218 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8145 (tt0) cc_final: 0.7776 (mt0)
REVERT: A  204 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8165 (mm110)
REVERT: A  238 ASN cc_start: 0.8919 (m110) cc_final: 0.8646 (m110)
REVERT: B   75 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8133 (tt0)
REVERT: R   54 HIS cc_start: 0.6976 (m170) cc_final: 0.6773 (m170)
REVERT: R  157 MET cc_start: 0.8017 (ttm) cc_final: 0.7589 (ttm)
REVERT: R  170 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8069 (tt)
REVERT: S   18 ARG cc_start: 0.8500 (tpp80) cc_final: 0.7979 (tpt90)
REVERT: Y   48 ASP cc_start: 0.8594 (t0) cc_final: 0.8300 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 142
  average time/residue: 0.2261
  time to fit residues: 43.4916
Evaluate side-chains
  137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  170 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0370
   chunk 78 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0870
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 261 GLN
B  32 GLN
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.150712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.116180 restraints weight = 10954.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.56
r_work: 0.3174 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8582  Z= 0.098
  Angle     :  0.507  10.538  11670  Z= 0.261
  Chirality :  0.041   0.143   1341
  Planarity :  0.003   0.036   1474
  Dihedral  :  3.968  20.065   1191
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.94 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1084
  helix:  2.55 (0.27), residues: 369
  sheet:  0.76 (0.33), residues: 251
  loop : -1.51 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.035   0.001   TYR R 287 
 ARG   0.008   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  376)
  hydrogen bonds       : angle       4.11297 ( 1077)
  SS BOND              : bond        0.00443 (    2)
  SS BOND              : angle       0.63373 (    4)
  covalent geometry    : bond        0.00204 ( 8580)
  covalent geometry    : angle       0.50734 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8125 (tt0) cc_final: 0.7815 (mt0)
REVERT: A  204 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8209 (mm110)
REVERT: A  238 ASN cc_start: 0.8876 (m110) cc_final: 0.8599 (m110)
REVERT: B   75 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8135 (tt0)
REVERT: R  157 MET cc_start: 0.7970 (ttm) cc_final: 0.7533 (ttm)
REVERT: R  170 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7913 (tt)
REVERT: S   18 ARG cc_start: 0.8434 (tpp80) cc_final: 0.7912 (tpt90)
REVERT: S   83 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.5999 (mmt)
  outliers start: 16
  outliers final: 8
  residues processed: 149
  average time/residue: 0.2120
  time to fit residues: 43.2230
Evaluate side-chains
  141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  125 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  294 SER
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue   83 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0040
   chunk 67 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 23 optimal weight:   30.0000
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0370
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.5470

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 261 GLN
B  32 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.151151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.116426 restraints weight = 10927.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.58
r_work: 0.3177 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8582  Z= 0.098
  Angle     :  0.506  10.306  11670  Z= 0.261
  Chirality :  0.041   0.138   1341
  Planarity :  0.003   0.038   1474
  Dihedral  :  3.854  17.376   1191
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.52 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1084
  helix:  2.69 (0.27), residues: 369
  sheet:  0.88 (0.33), residues: 250
  loop : -1.41 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.027   0.001   TYR R 287 
 ARG   0.009   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  376)
  hydrogen bonds       : angle       4.02955 ( 1077)
  SS BOND              : bond        0.00357 (    2)
  SS BOND              : angle       0.77089 (    4)
  covalent geometry    : bond        0.00207 ( 8580)
  covalent geometry    : angle       0.50584 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8123 (tt0) cc_final: 0.7803 (mt0)
REVERT: A  204 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8226 (mm110)
REVERT: A  238 ASN cc_start: 0.8881 (m110) cc_final: 0.8599 (m110)
REVERT: B   75 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8127 (tt0)
REVERT: R  157 MET cc_start: 0.7972 (ttm) cc_final: 0.7519 (ttm)
REVERT: S   18 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8004 (tpt170)
REVERT: S   83 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6003 (mmt)
REVERT: Y   48 ASP cc_start: 0.8688 (t0) cc_final: 0.8421 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 149
  average time/residue: 0.2010
  time to fit residues: 40.8711
Evaluate side-chains
  145 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  125 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  294 SER
Chi-restraints excluded: chain R residue  296 LEU
Chi-restraints excluded: chain S residue   83 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 103 optimal weight:    0.4980
   chunk 97 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
B  32 GLN
B 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.151318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.117532 restraints weight = 10900.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.66
r_work: 0.3200 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8582  Z= 0.107
  Angle     :  0.518   9.849  11670  Z= 0.267
  Chirality :  0.041   0.135   1341
  Planarity :  0.003   0.039   1474
  Dihedral  :  3.873  17.305   1191
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.40 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1084
  helix:  2.65 (0.27), residues: 369
  sheet:  0.94 (0.33), residues: 248
  loop : -1.37 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.023   0.001   PHE R 207 
 TYR   0.026   0.001   TYR R 287 
 ARG   0.006   0.000   ARG Y  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04007 (  376)
  hydrogen bonds       : angle       4.02306 ( 1077)
  SS BOND              : bond        0.00576 (    2)
  SS BOND              : angle       1.07630 (    4)
  covalent geometry    : bond        0.00234 ( 8580)
  covalent geometry    : angle       0.51749 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.982 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8132 (tt0) cc_final: 0.7814 (mt0)
REVERT: A  204 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8231 (mm110)
REVERT: A  238 ASN cc_start: 0.8890 (m110) cc_final: 0.8628 (m110)
REVERT: B   75 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8107 (tt0)
REVERT: R  157 MET cc_start: 0.8048 (ttm) cc_final: 0.7611 (ttm)
REVERT: S   18 ARG cc_start: 0.8439 (tpp80) cc_final: 0.7987 (tpt170)
REVERT: S   83 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6049 (mmt)
REVERT: Y   48 ASP cc_start: 0.8638 (t0) cc_final: 0.8359 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 146
  average time/residue: 0.2103
  time to fit residues: 41.8721
Evaluate side-chains
  149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  294 SER
Chi-restraints excluded: chain R residue  296 LEU
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 7 optimal weight:    0.0870
   chunk 64 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 83 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0040
   chunk 59 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.8174

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
B  32 GLN
B 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.150184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.115263 restraints weight = 10895.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.57
r_work: 0.3197 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8582  Z= 0.106
  Angle     :  0.513   9.221  11670  Z= 0.265
  Chirality :  0.041   0.131   1341
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.833  17.336   1191
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.57 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1084
  helix:  2.63 (0.27), residues: 371
  sheet:  0.93 (0.33), residues: 248
  loop : -1.32 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.018   0.001   PHE R 207 
 TYR   0.021   0.001   TYR R 287 
 ARG   0.005   0.000   ARG Y  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  376)
  hydrogen bonds       : angle       4.01136 ( 1077)
  SS BOND              : bond        0.00550 (    2)
  SS BOND              : angle       0.87325 (    4)
  covalent geometry    : bond        0.00231 ( 8580)
  covalent geometry    : angle       0.51261 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8135 (tt0) cc_final: 0.7813 (mt0)
REVERT: A  238 ASN cc_start: 0.8881 (m110) cc_final: 0.8614 (m110)
REVERT: B   75 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8100 (tt0)
REVERT: R  157 MET cc_start: 0.8066 (ttm) cc_final: 0.7247 (ttp)
REVERT: S   18 ARG cc_start: 0.8372 (tpp80) cc_final: 0.7908 (tpt170)
REVERT: S   83 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6042 (mmt)
REVERT: Y   48 ASP cc_start: 0.8637 (t0) cc_final: 0.8337 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 146
  average time/residue: 0.2046
  time to fit residues: 40.8711
Evaluate side-chains
  146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  100 SER
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  296 LEU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 23 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0970
   chunk 108 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 197 HIS
B  32 GLN
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.150729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.115897 restraints weight = 10953.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.57
r_work: 0.3203 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8582  Z= 0.100
  Angle     :  0.503   8.432  11670  Z= 0.260
  Chirality :  0.041   0.133   1341
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.789  17.246   1191
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.80 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1084
  helix:  2.63 (0.27), residues: 371
  sheet:  0.96 (0.33), residues: 248
  loop : -1.28 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.018   0.001   PHE R 207 
 TYR   0.021   0.001   TYR R 287 
 ARG   0.005   0.000   ARG Y  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (  376)
  hydrogen bonds       : angle       3.99056 ( 1077)
  SS BOND              : bond        0.00525 (    2)
  SS BOND              : angle       0.79909 (    4)
  covalent geometry    : bond        0.00214 ( 8580)
  covalent geometry    : angle       0.50272 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8089 (tt0) cc_final: 0.7777 (mt0)
REVERT: A  238 ASN cc_start: 0.8881 (m110) cc_final: 0.8614 (m110)
REVERT: B   75 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8106 (tt0)
REVERT: B  258 ASP cc_start: 0.7673 (t0) cc_final: 0.7440 (t0)
REVERT: R  157 MET cc_start: 0.8072 (ttm) cc_final: 0.7260 (ttp)
REVERT: S   18 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7906 (tpt170)
REVERT: S   83 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6001 (mmt)
REVERT: Y   48 ASP cc_start: 0.8642 (t0) cc_final: 0.8324 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 148
  average time/residue: 0.1960
  time to fit residues: 40.1386
Evaluate side-chains
  147 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  100 SER
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  296 LEU
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 70 optimal weight:    6.9990
   chunk 99 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 197 HIS
B  32 GLN
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.149371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.114489 restraints weight = 10825.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.59
r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8582  Z= 0.111
  Angle     :  0.519   8.530  11670  Z= 0.271
  Chirality :  0.042   0.134   1341
  Planarity :  0.004   0.044   1474
  Dihedral  :  3.855  17.396   1191
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.38 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1084
  helix:  2.58 (0.27), residues: 372
  sheet:  0.84 (0.33), residues: 255
  loop : -1.28 (0.26), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R  59 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.017   0.001   PHE R 207 
 TYR   0.031   0.001   TYR R 287 
 ARG   0.005   0.000   ARG Y  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  376)
  hydrogen bonds       : angle       4.04313 ( 1077)
  SS BOND              : bond        0.00602 (    2)
  SS BOND              : angle       0.94398 (    4)
  covalent geometry    : bond        0.00246 ( 8580)
  covalent geometry    : angle       0.51919 (11666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8153 (tt0) cc_final: 0.7851 (mt0)
REVERT: A  238 ASN cc_start: 0.8893 (m110) cc_final: 0.8629 (m110)
REVERT: B   75 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8121 (tt0)
REVERT: R  157 MET cc_start: 0.8071 (ttm) cc_final: 0.7266 (ttp)
REVERT: S   18 ARG cc_start: 0.8386 (tpp80) cc_final: 0.7914 (tpt170)
REVERT: S   83 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6100 (mmt)
REVERT: Y   48 ASP cc_start: 0.8624 (t0) cc_final: 0.8300 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 144
  average time/residue: 0.2163
  time to fit residues: 42.2855
Evaluate side-chains
  143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  100 SER
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  296 LEU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 90 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 95 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 197 HIS
B  32 GLN
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.149534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.115331 restraints weight = 10868.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.53
r_work: 0.3172 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8582  Z= 0.121
  Angle     :  0.535   8.773  11670  Z= 0.277
  Chirality :  0.042   0.137   1341
  Planarity :  0.004   0.045   1474
  Dihedral  :  3.955  17.615   1191
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.73 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1084
  helix:  2.57 (0.27), residues: 372
  sheet:  0.82 (0.33), residues: 255
  loop : -1.28 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  59 
 HIS   0.009   0.001   HIS R  62 
 PHE   0.018   0.001   PHE R 207 
 TYR   0.035   0.001   TYR R 287 
 ARG   0.005   0.000   ARG Y  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  376)
  hydrogen bonds       : angle       4.11315 ( 1077)
  SS BOND              : bond        0.00663 (    2)
  SS BOND              : angle       1.02672 (    4)
  covalent geometry    : bond        0.00277 ( 8580)
  covalent geometry    : angle       0.53447 (11666)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5435.93 seconds
wall clock time: 94 minutes 20.99 seconds (5660.99 seconds total)