Starting phenix.real_space_refine
on Fri Jun  6 17:12:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wu9_32824/06_2025/7wu9_32824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wu9_32824/06_2025/7wu9_32824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.375
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wu9_32824/06_2025/7wu9_32824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wu9_32824/06_2025/7wu9_32824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wu9_32824/06_2025/7wu9_32824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wu9_32824/06_2025/7wu9_32824.cif"
  }
  resolution = 3.375
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 780 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    4645      2.51       5
     N    1279      2.21       5
     O    1398      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7369
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1758
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 274, 1753
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 111}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 265}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 417
          Unresolved non-hydrogen angles: 529
          Unresolved non-hydrogen dihedrals: 345
          Unresolved non-hydrogen chiralities: 56
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 2, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 180
      Conformer: "B"
        Number of residues, atoms: 274, 1753
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 111}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 265}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 417
          Unresolved non-hydrogen angles: 529
          Unresolved non-hydrogen dihedrals: 345
          Unresolved non-hydrogen chiralities: 56
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 2, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 180
          bond proxies already assigned to first conformer: 1776
    Chain: "A"
      Number of atoms: 1018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1018
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'TRANS': 134}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 48
    Chain: "B"
      Number of atoms: 2487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2487
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 119
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 71
    Chain: "G"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 345
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "S"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1761
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE R 236 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BPHE R 236 " occ=0.50
  Time building chain proxies: 6.14, per 1000 atoms: 0.83
  Number of scatterers: 7369
  At special positions: 0
  Unit cell: (116.1, 118.8, 95.175, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1398      8.00
     N    1279      7.00
     C    4645      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 130 " - pdb=" SG  CYS R 208 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.87
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 14 sheets defined
      38.2% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'R' and resid 52 through 75
      removed outlier: 4.254A  pdb=" N   ILE R  56 " --> pdb=" O   VAL R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 116
      removed outlier: 3.613A  pdb=" N   LEU R  89 " --> pdb=" O   LYS R  85 " (cutoff:3.500A)
      Proline residue:  R 108  - end of helix
    Processing helix  chain 'R' and resid 127 through 161
      removed outlier: 3.532A  pdb=" N   LEU R 145 " --> pdb=" O   GLY R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 169
      removed outlier: 3.790A  pdb=" N   ALA R 166 " --> pdb=" O   PRO R 162 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   SER R 167 " --> pdb=" O   HIS R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 170 through 195
      removed outlier: 3.574A  pdb=" N   ARG R 175 " --> pdb=" O   THR R 171 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL R 181 " --> pdb=" O   VAL R 177 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TRP R 182 " --> pdb=" O   LEU R 178 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU R 183 " --> pdb=" O   LEU R 179 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU R 191 " --> pdb=" O   ALA R 187 " (cutoff:3.500A)
      Proline residue:  R 192  - end of helix
    Processing helix  chain 'R' and resid 227 through 265
      removed outlier: 3.561A  pdb=" N   ALA R 231 " --> pdb=" O   ASN R 227 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   SER R 232 " --> pdb=" O   LEU R 228 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR R 265 " --> pdb=" O   ARG R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 271 through 308
      removed outlier: 3.711A  pdb=" N   ILE R 276 " --> pdb=" O   GLN R 272 " (cutoff:3.500A)
      Proline residue:  R 297  - end of helix
    Processing helix  chain 'R' and resid 324 through 347
      removed outlier: 4.087A  pdb=" N   PHE R 328 " --> pdb=" O   GLU R 324 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ARG R 333 " --> pdb=" O   LEU R 329 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASN R 338 " --> pdb=" O   LEU R 334 " (cutoff:3.500A)
      Proline residue:  R 343  - end of helix
      removed outlier: 3.799A  pdb=" N   TYR R 346 " --> pdb=" O   ASP R 342 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 347 through 357
      removed outlier: 3.898A  pdb=" N   LYS R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE R 352 " --> pdb=" O   LEU R 348 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG R 355 " --> pdb=" O   LYS R 351 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE R 357 " --> pdb=" O   LEU R 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.861A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 210
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.858A  pdb=" N   PHE A 215 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 255
      removed outlier: 3.776A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 3.923A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 3.729A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.854A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'G' and resid 10 through 22
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.524A  pdb=" N   CYS G  41 " --> pdb=" O   LEU G  37 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.503A  pdb=" N   GLU G  58 " --> pdb=" O   PRO G  55 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 62 through 65
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.604A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'R' and resid 199 through 201
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 188
      removed outlier: 3.801A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 52
      removed outlier: 4.079A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.510A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.519A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 152
      removed outlier: 3.841A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.054A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.463A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.084A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.544A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.521A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 148
      removed outlier: 6.101A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 147 through 148
      removed outlier: 6.101A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN S 231 " --> pdb=" O   THR S 238 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   THR S 238 " --> pdb=" O   GLN S 231 " (cutoff:3.500A)

    391 hydrogen bonds defined for protein.
    1087 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: 2.09

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2437
        1.34 -     1.46: 1815
        1.46 -     1.58: 3192
        1.58 -     1.69: 0
        1.69 -     1.81: 65
  Bond restraints: 7509
  Sorted by residual:
  bond pdb=" CA  HIS A 195 "
       pdb=" C   HIS A 195 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.008 1.10e-02 8.26e+03 5.32e-01
  bond pdb=" CG  ARG R 350 "
       pdb=" CD  ARG R 350 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 4.76e-01
  bond pdb=" CB  PRO S 236 "
       pdb=" CG  PRO S 236 "
    ideal  model  delta    sigma   weight residual
    1.506  1.481  0.025 3.90e-02 6.57e+02 4.25e-01
  bond pdb=" CB  LYS A  29 "
       pdb=" CG  LYS A  29 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 3.00e-02 1.11e+03 4.22e-01
  bond pdb=" CB  ARG R 350 "
       pdb=" CG  ARG R 350 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 3.00e-02 1.11e+03 4.10e-01
  ... (remaining 7504 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 9845
        0.92 -     1.85: 320
        1.85 -     2.77: 38
        2.77 -     3.69: 25
        3.69 -     4.62: 12
  Bond angle restraints: 10240
  Sorted by residual:
  angle pdb=" CA  HIS A 195 "
        pdb=" C   HIS A 195 "
        pdb=" O   HIS A 195 "
      ideal   model   delta    sigma   weight residual
     122.64  120.41    2.23 1.25e+00 6.40e-01 3.19e+00
  angle pdb=" CA  TYR S 190 "
        pdb=" CB  TYR S 190 "
        pdb=" CG  TYR S 190 "
      ideal   model   delta    sigma   weight residual
     113.90  117.01   -3.11 1.80e+00 3.09e-01 2.99e+00
  angle pdb=" CA  HIS A 195 "
        pdb=" C   HIS A 195 "
        pdb=" N   PHE A 196 "
      ideal   model   delta    sigma   weight residual
     114.76  116.67   -1.91 1.14e+00 7.69e-01 2.81e+00
  angle pdb=" CA  GLN S  13 "
        pdb=" CB  GLN S  13 "
        pdb=" CG  GLN S  13 "
      ideal   model   delta    sigma   weight residual
     114.10  117.43   -3.33 2.00e+00 2.50e-01 2.78e+00
  angle pdb=" CB  ARG R 350 "
        pdb=" CG  ARG R 350 "
        pdb=" CD  ARG R 350 "
      ideal   model   delta    sigma   weight residual
     111.30  115.03   -3.73 2.30e+00 1.89e-01 2.62e+00
  ... (remaining 10235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4014
       17.97 -    35.94: 292
       35.94 -    53.91: 56
       53.91 -    71.88: 4
       71.88 -    89.85: 5
  Dihedral angle restraints: 4371
    sinusoidal: 1406
      harmonic: 2965
  Sorted by residual:
  dihedral pdb=" CB  CYS R 130 "
           pdb=" SG  CYS R 130 "
           pdb=" SG  CYS R 208 "
           pdb=" CB  CYS R 208 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.77   70.77     1      1.00e+01 1.00e-02 6.44e+01
  dihedral pdb=" CA  PHE S  32 "
           pdb=" C   PHE S  32 "
           pdb=" N   GLY S  33 "
           pdb=" CA  GLY S  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  THR B 179 "
           pdb=" C   THR B 179 "
           pdb=" N   PHE B 180 "
           pdb=" CA  PHE B 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.01   15.99     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 4368 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 786
       0.029 -    0.058: 288
       0.058 -    0.087: 69
       0.087 -    0.116: 51
       0.116 -    0.145: 20
  Chirality restraints: 1214
  Sorted by residual:
  chirality pdb=" CA  ILE S 189 "
            pdb=" N   ILE S 189 "
            pdb=" C   ILE S 189 "
            pdb=" CB  ILE S 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 1211 not shown)

  Planarity restraints: 1309
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO G  49 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.021 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO B 236 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 234 "    0.010 2.00e-02 2.50e+03   8.76e-03 1.34e+00
        pdb=" CG  PHE B 234 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 234 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 234 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 234 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 234 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 234 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1306 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 199
        2.69 -     3.24: 7472
        3.24 -     3.79: 11242
        3.79 -     4.35: 14713
        4.35 -     4.90: 24981
  Nonbonded interactions: 58607
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   ASP A 337 "
            pdb=" OG1 THR A 340 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OH  TYR S 101 "
            pdb=" NE2 HIS S 232 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.248 3.040
  ... (remaining 58602 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=0.50 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:             3.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.260
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
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      :  0.002   0.025   7510  Z= 0.105
  Angle     :  0.424   4.615  10242  Z= 0.227
  Chirality :  0.039   0.145   1214
  Planarity :  0.002   0.032   1309
  Dihedral  : 13.281  89.849   2448
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.28), residues: 1003
  helix:  3.10 (0.28), residues: 341
  sheet: -0.68 (0.30), residues: 303
  loop : -0.02 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.002   0.000   HIS B  91 
 PHE   0.020   0.001   PHE B 234 
 TYR   0.017   0.001   TYR S 190 
 ARG   0.003   0.000   ARG R 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23523 (  389)
  hydrogen bonds       : angle       7.57660 ( 1087)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.22899 (    2)
  covalent geometry    : bond        0.00240 ( 7509)
  covalent geometry    : angle       0.42400 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   70 MET cc_start: 0.7619 (mpp) cc_final: 0.7262 (mpp)
REVERT: R  203 TRP cc_start: 0.8385 (t60) cc_final: 0.8019 (t60)
REVERT: R  325 CYS cc_start: 0.9075 (p) cc_final: 0.8612 (p)
REVERT: A  197 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8021 (mtpp)
REVERT: B  130 GLU cc_start: 0.8061 (pm20) cc_final: 0.7632 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2527
  time to fit residues: 56.7209
Evaluate side-chains
  142 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0170
   overall best weight:    1.5824

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
G  59 ASN
S 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.181778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.113075 restraints weight = 9514.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 3.26
r_work: 0.2964 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7510  Z= 0.222
  Angle     :  0.622  11.104  10242  Z= 0.323
  Chirality :  0.045   0.178   1214
  Planarity :  0.004   0.040   1309
  Dihedral  :  4.033  26.765   1085
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.62 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.27), residues: 1003
  helix:  2.68 (0.27), residues: 349
  sheet: -0.43 (0.30), residues: 297
  loop : -0.29 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP R 207 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.023   0.002   PHE B 180 
 TYR   0.025   0.002   TYR S 190 
 ARG   0.005   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05038 (  389)
  hydrogen bonds       : angle       5.06097 ( 1087)
  SS BOND              : bond        0.00751 (    1)
  SS BOND              : angle       2.33825 (    2)
  covalent geometry    : bond        0.00518 ( 7509)
  covalent geometry    : angle       0.62115 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.767 
Fit side-chains
REVERT: R   94 TRP cc_start: 0.8541 (t60) cc_final: 0.8235 (t60)
REVERT: R  203 TRP cc_start: 0.8714 (t60) cc_final: 0.8181 (t60)
REVERT: A   35 LYS cc_start: 0.8529 (mptt) cc_final: 0.8307 (mptt)
REVERT: A  197 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7804 (mtpp)
  outliers start: 10
  outliers final: 7
  residues processed: 165
  average time/residue: 0.2334
  time to fit residues: 49.1043
Evaluate side-chains
  146 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 26 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 63 optimal weight:    0.1980
   chunk 48 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.182260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.113632 restraints weight = 9666.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 3.29
r_work: 0.2976 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7510  Z= 0.165
  Angle     :  0.574  11.378  10242  Z= 0.298
  Chirality :  0.044   0.159   1214
  Planarity :  0.003   0.041   1309
  Dihedral  :  3.950  30.069   1085
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.49 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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 (0.27), residues: 1003
  helix:  2.48 (0.27), residues: 350
  sheet: -0.43 (0.30), residues: 298
  loop : -0.29 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.016   0.002   PHE B 180 
 TYR   0.021   0.001   TYR S 190 
 ARG   0.006   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04095 (  389)
  hydrogen bonds       : angle       4.67367 ( 1087)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       1.11442 (    2)
  covalent geometry    : bond        0.00383 ( 7509)
  covalent geometry    : angle       0.57385 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.760 
Fit side-chains
REVERT: R   84 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.6664 (mmp-170)
REVERT: R   94 TRP cc_start: 0.8568 (t60) cc_final: 0.8353 (t60)
REVERT: R  203 TRP cc_start: 0.8725 (t60) cc_final: 0.8202 (t60)
REVERT: A  197 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7643 (mtpp)
REVERT: B  127 LYS cc_start: 0.8851 (mttp) cc_final: 0.8581 (mtpt)
  outliers start: 14
  outliers final: 10
  residues processed: 149
  average time/residue: 0.2454
  time to fit residues: 46.3849
Evaluate side-chains
  144 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:   20.0000
   chunk 14 optimal weight:   30.0000
   chunk 7 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    3.5986

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.176647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.101069 restraints weight = 9752.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.97
r_work: 0.2889 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2588 r_free = 0.2588    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2588 r_free = 0.2588    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.078   7510  Z= 0.429
  Angle     :  0.735  12.181  10242  Z= 0.384
  Chirality :  0.049   0.222   1214
  Planarity :  0.004   0.046   1309
  Dihedral  :  4.569  41.523   1085
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.94 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.58 (0.27), residues: 1003
  helix:  2.32 (0.27), residues: 346
  sheet: -0.61 (0.30), residues: 293
  loop : -0.57 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP R 207 
 HIS   0.006   0.002   HIS B 183 
 PHE   0.036   0.002   PHE B 180 
 TYR   0.028   0.003   TYR S 190 
 ARG   0.008   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04641 (  389)
  hydrogen bonds       : angle       4.79469 ( 1087)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.93516 (    2)
  covalent geometry    : bond        0.01018 ( 7509)
  covalent geometry    : angle       0.73504 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.760 
Fit side-chains
REVERT: R   70 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7377 (mpp)
REVERT: R   84 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.6712 (mmp-170)
REVERT: R   94 TRP cc_start: 0.8542 (t60) cc_final: 0.8300 (t60)
REVERT: R  169 MET cc_start: 0.6964 (tmm) cc_final: 0.6657 (tmm)
REVERT: R  203 TRP cc_start: 0.8799 (t60) cc_final: 0.8220 (t60)
REVERT: B  262 MET cc_start: 0.8089 (tpp) cc_final: 0.7670 (tpp)
REVERT: S   18 ARG cc_start: 0.7656 (tpt-90) cc_final: 0.7174 (tpp80)
  outliers start: 21
  outliers final: 17
  residues processed: 150
  average time/residue: 0.2542
  time to fit residues: 48.0934
Evaluate side-chains
  159 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   70 MET
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0070
   chunk 64 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.182503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.112255 restraints weight = 9562.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 3.27
r_work: 0.2965 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2846
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2846 r_free = 0.2846    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2846 r_free = 0.2846    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2846
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7510  Z= 0.134
  Angle     :  0.573  10.493  10242  Z= 0.295
  Chirality :  0.043   0.162   1214
  Planarity :  0.003   0.042   1309
  Dihedral  :  4.070  35.403   1085
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.80 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 1003
  helix:  2.36 (0.28), residues: 346
  sheet: -0.56 (0.30), residues: 297
  loop : -0.36 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP R 207 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 209 
 TYR   0.019   0.001   TYR S 190 
 ARG   0.008   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  389)
  hydrogen bonds       : angle       4.48924 ( 1087)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.54606 (    2)
  covalent geometry    : bond        0.00307 ( 7509)
  covalent geometry    : angle       0.57332 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: R   84 ARG cc_start: 0.7409 (ttp-170) cc_final: 0.6745 (mmp-170)
REVERT: R  203 TRP cc_start: 0.8750 (t60) cc_final: 0.8225 (t60)
REVERT: A   25 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7225 (mm-30)
REVERT: B  262 MET cc_start: 0.7861 (tpp) cc_final: 0.7345 (tpp)
REVERT: S   18 ARG cc_start: 0.7626 (tpt-90) cc_final: 0.7243 (tpp80)
REVERT: S  202 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7552 (mtm110)
  outliers start: 19
  outliers final: 14
  residues processed: 168
  average time/residue: 0.2463
  time to fit residues: 52.5459
Evaluate side-chains
  163 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   70 MET
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0670
   chunk 41 optimal weight:    7.9990
   chunk 95 optimal weight:    0.5980
   chunk 65 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7324

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.182780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.113928 restraints weight = 9612.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 3.25
r_work: 0.2989 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7510  Z= 0.136
  Angle     :  0.571  10.235  10242  Z= 0.293
  Chirality :  0.043   0.166   1214
  Planarity :  0.003   0.042   1309
  Dihedral  :  3.940  33.855   1085
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.95 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.79 (0.27), residues: 1003
  helix:  2.42 (0.28), residues: 345
  sheet: -0.51 (0.29), residues: 301
  loop : -0.34 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE S  27 
 TYR   0.019   0.001   TYR S 190 
 ARG   0.008   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  389)
  hydrogen bonds       : angle       4.37984 ( 1087)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.50965 (    2)
  covalent geometry    : bond        0.00312 ( 7509)
  covalent geometry    : angle       0.57127 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.829 
Fit side-chains
REVERT: R   84 ARG cc_start: 0.7403 (ttp-170) cc_final: 0.6782 (mmp-170)
REVERT: R   94 TRP cc_start: 0.8529 (t60) cc_final: 0.8124 (t60)
REVERT: R  188 PHE cc_start: 0.7434 (t80) cc_final: 0.7186 (t80)
REVERT: R  203 TRP cc_start: 0.8731 (t60) cc_final: 0.8282 (t60)
REVERT: R  357 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5097 (t80)
REVERT: A   25 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7055 (mt-10)
REVERT: B  228 ASP cc_start: 0.8319 (m-30) cc_final: 0.7651 (m-30)
REVERT: B  262 MET cc_start: 0.7857 (tpp) cc_final: 0.7314 (tpp)
REVERT: S   18 ARG cc_start: 0.7664 (tpt-90) cc_final: 0.7248 (tpp80)
REVERT: S  202 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7582 (mtm110)
  outliers start: 19
  outliers final: 14
  residues processed: 165
  average time/residue: 0.2447
  time to fit residues: 51.4500
Evaluate side-chains
  159 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain R residue  357 PHE
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 0 optimal weight:   30.0000
   chunk 51 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.183609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.114212 restraints weight = 9574.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 3.33
r_work: 0.2987 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7510  Z= 0.133
  Angle     :  0.569  11.207  10242  Z= 0.291
  Chirality :  0.043   0.178   1214
  Planarity :  0.003   0.042   1309
  Dihedral  :  3.855  33.070   1085
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.38 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.80 (0.27), residues: 1003
  helix:  2.35 (0.27), residues: 346
  sheet: -0.47 (0.29), residues: 301
  loop : -0.27 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.021   0.001   PHE A 334 
 TYR   0.019   0.001   TYR S 190 
 ARG   0.009   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  389)
  hydrogen bonds       : angle       4.30624 ( 1087)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.49142 (    2)
  covalent geometry    : bond        0.00307 ( 7509)
  covalent geometry    : angle       0.56892 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.842 
Fit side-chains
REVERT: R   84 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6776 (mmp-170)
REVERT: R   94 TRP cc_start: 0.8401 (t60) cc_final: 0.8194 (t60)
REVERT: R  188 PHE cc_start: 0.7366 (t80) cc_final: 0.7128 (t80)
REVERT: R  203 TRP cc_start: 0.8730 (t60) cc_final: 0.8317 (t60)
REVERT: R  357 PHE cc_start: 0.5975 (OUTLIER) cc_final: 0.5129 (t80)
REVERT: A   25 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6990 (mt-10)
REVERT: B  220 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7435 (mp10)
REVERT: B  228 ASP cc_start: 0.8322 (m-30) cc_final: 0.7653 (m-30)
REVERT: B  262 MET cc_start: 0.7856 (tpp) cc_final: 0.7393 (tpp)
REVERT: S   18 ARG cc_start: 0.7639 (tpt-90) cc_final: 0.7151 (tpp80)
REVERT: S   89 GLU cc_start: 0.8484 (pm20) cc_final: 0.8196 (tm-30)
REVERT: S  202 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7533 (mtm110)
  outliers start: 21
  outliers final: 14
  residues processed: 163
  average time/residue: 0.2481
  time to fit residues: 51.9007
Evaluate side-chains
  159 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain R residue  357 PHE
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 73 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0370
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.1262

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.182913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.108193 restraints weight = 9720.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 3.06
r_work: 0.2997 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7510  Z= 0.167
  Angle     :  0.607  11.585  10242  Z= 0.307
  Chirality :  0.044   0.183   1214
  Planarity :  0.003   0.043   1309
  Dihedral  :  3.941  35.607   1085
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.39 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.80 (0.27), residues: 1003
  helix:  2.40 (0.27), residues: 342
  sheet: -0.49 (0.29), residues: 301
  loop : -0.29 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.002   PHE B 180 
 TYR   0.021   0.001   TYR S 190 
 ARG   0.009   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03513 (  389)
  hydrogen bonds       : angle       4.31660 ( 1087)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.40626 (    2)
  covalent geometry    : bond        0.00393 ( 7509)
  covalent geometry    : angle       0.60711 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.895 
Fit side-chains
REVERT: R   84 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.6784 (mmp-170)
REVERT: R   94 TRP cc_start: 0.8427 (t60) cc_final: 0.8201 (t60)
REVERT: R  203 TRP cc_start: 0.8737 (t60) cc_final: 0.8317 (t60)
REVERT: R  357 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5140 (t80)
REVERT: A   25 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7009 (mt-10)
REVERT: B  220 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7401 (mp10)
REVERT: B  228 ASP cc_start: 0.8419 (m-30) cc_final: 0.7651 (m-30)
REVERT: B  262 MET cc_start: 0.7837 (tpp) cc_final: 0.7408 (tpp)
REVERT: S   18 ARG cc_start: 0.7676 (tpt-90) cc_final: 0.7452 (tpp80)
REVERT: S   89 GLU cc_start: 0.8470 (pm20) cc_final: 0.8199 (tm-30)
REVERT: S  202 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7542 (mtm110)
  outliers start: 19
  outliers final: 16
  residues processed: 158
  average time/residue: 0.2825
  time to fit residues: 58.8906
Evaluate side-chains
  163 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain R residue  357 PHE
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.180876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.105990 restraints weight = 9778.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 3.00
r_work: 0.2962 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   7510  Z= 0.233
  Angle     :  0.652  12.272  10242  Z= 0.331
  Chirality :  0.045   0.191   1214
  Planarity :  0.004   0.043   1309
  Dihedral  :  4.182  40.681   1085
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.39 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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 (0.27), residues: 1003
  helix:  2.35 (0.27), residues: 345
  sheet: -0.54 (0.30), residues: 296
  loop : -0.37 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP R 207 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.022   0.002   PHE B 180 
 TYR   0.023   0.002   TYR S 190 
 ARG   0.009   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  389)
  hydrogen bonds       : angle       4.40465 ( 1087)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.40265 (    2)
  covalent geometry    : bond        0.00553 ( 7509)
  covalent geometry    : angle       0.65253 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.861 
Fit side-chains
REVERT: R   84 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.6773 (mmp-170)
REVERT: R   94 TRP cc_start: 0.8439 (t60) cc_final: 0.8232 (t60)
REVERT: R  203 TRP cc_start: 0.8759 (t60) cc_final: 0.8301 (t60)
REVERT: R  357 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.5120 (t80)
REVERT: A   25 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7069 (mt-10)
REVERT: B  220 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7366 (mp10)
REVERT: B  228 ASP cc_start: 0.8489 (m-30) cc_final: 0.7705 (m-30)
REVERT: B  262 MET cc_start: 0.7879 (tpp) cc_final: 0.7458 (tpp)
REVERT: G   48 ASP cc_start: 0.8661 (t0) cc_final: 0.8446 (t0)
REVERT: S   89 GLU cc_start: 0.8498 (pm20) cc_final: 0.8204 (tm-30)
REVERT: S  202 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7777 (mtm110)
  outliers start: 22
  outliers final: 20
  residues processed: 154
  average time/residue: 0.2901
  time to fit residues: 56.5840
Evaluate side-chains
  158 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain R residue  357 PHE
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0970
   chunk 5 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0770
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.5736

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.184180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.115320 restraints weight = 9756.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 3.33
r_work: 0.2999 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7510  Z= 0.130
  Angle     :  0.611  11.806  10242  Z= 0.308
  Chirality :  0.044   0.188   1214
  Planarity :  0.004   0.042   1309
  Dihedral  :  4.000  37.847   1085
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.67 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.80 (0.27), residues: 1003
  helix:  2.31 (0.27), residues: 346
  sheet: -0.47 (0.30), residues: 301
  loop : -0.23 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP R 207 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 234 
 TYR   0.019   0.001   TYR S 190 
 ARG   0.010   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  389)
  hydrogen bonds       : angle       4.34821 ( 1087)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.31005 (    2)
  covalent geometry    : bond        0.00298 ( 7509)
  covalent geometry    : angle       0.61057 (10240)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.845 
Fit side-chains
REVERT: R   84 ARG cc_start: 0.7452 (ttp-170) cc_final: 0.6810 (mmp-170)
REVERT: R  203 TRP cc_start: 0.8726 (t60) cc_final: 0.8324 (t60)
REVERT: R  357 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5160 (t80)
REVERT: A   25 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7006 (mt-10)
REVERT: B  130 GLU cc_start: 0.8439 (pm20) cc_final: 0.8045 (pm20)
REVERT: B  220 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7368 (mp10)
REVERT: B  228 ASP cc_start: 0.8435 (m-30) cc_final: 0.7692 (m-30)
REVERT: B  262 MET cc_start: 0.7841 (tpp) cc_final: 0.7442 (tpp)
REVERT: G   48 ASP cc_start: 0.8675 (t0) cc_final: 0.8411 (t0)
REVERT: S   18 ARG cc_start: 0.7725 (tpp80) cc_final: 0.6886 (tpt-90)
REVERT: S   89 GLU cc_start: 0.8477 (pm20) cc_final: 0.8196 (tm-30)
REVERT: S  140 MET cc_start: 0.8244 (mtp) cc_final: 0.7987 (mtp)
  outliers start: 21
  outliers final: 17
  residues processed: 152
  average time/residue: 0.2719
  time to fit residues: 52.8825
Evaluate side-chains
  155 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 LEU
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  298 LEU
Chi-restraints excluded: chain R residue  357 PHE
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  186 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0070
   chunk 67 optimal weight:    0.5980
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 25 optimal weight:   20.0000
   chunk 90 optimal weight:    0.0030
   chunk 12 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.5210

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.184749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.111961 restraints weight = 9615.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.32
r_work: 0.3004 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7510  Z= 0.124
  Angle     :  0.603  11.785  10242  Z= 0.306
  Chirality :  0.044   0.201   1214
  Planarity :  0.004   0.041   1309
  Dihedral  :  3.920  36.582   1085
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.10 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.81 (0.27), residues: 1003
  helix:  2.24 (0.27), residues: 349
  sheet: -0.44 (0.29), residues: 301
  loop : -0.17 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP R 207 
 HIS   0.004   0.000   HIS S  35 
 PHE   0.016   0.001   PHE A 259 
 TYR   0.018   0.001   TYR S 190 
 ARG   0.009   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  389)
  hydrogen bonds       : angle       4.33705 ( 1087)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.23293 (    2)
  covalent geometry    : bond        0.00282 ( 7509)
  covalent geometry    : angle       0.60296 (10240)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5566.85 seconds
wall clock time: 96 minutes 49.64 seconds (5809.64 seconds total)