Starting phenix.real_space_refine
on Fri Jul 25 21:01:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p9x_20277/07_2025/6p9x_20277.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p9x_20277/07_2025/6p9x_20277.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p9x_20277/07_2025/6p9x_20277.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p9x_20277/07_2025/6p9x_20277.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p9x_20277/07_2025/6p9x_20277.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p9x_20277/07_2025/6p9x_20277.cif"
  }
  resolution = 2.91
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    5198      2.51       5
     N    1435      2.21       5
     O    1495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8177
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1638
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 192, 1627
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 185}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 192, 1627
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 185}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 1648
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2267
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 270, 2256
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 7, 'TRANS': 262}
      Conformer: "B"
        Number of residues, atoms: 270, 2256
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 7, 'TRANS': 262}
          bond proxies already assigned to first conformer: 2316
    Chain: "P"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 265
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 2, 'TRANS': 30}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "R"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "P"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  AARG A  38 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  38 " occ=0.50
    residue:
      pdb=" N   SER R 301 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER R 301 " occ=0.00
    residue:
      pdb=" N   THR R 302 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR R 302 " occ=0.00
    residue:
      pdb=" N   THR R 303 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR R 303 " occ=0.00
    residue:
      pdb=" N   GLY R 335 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY R 335 " occ=0.00
    residue:
      pdb=" N   GLU R 336 " occ=0.00
      ... (7 atoms not shown)
      pdb=" OE2 GLU R 336 " occ=0.00
    residue:
      pdb=" N  APHE R 362 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE R 362 " occ=0.50
  Time building chain proxies: 6.41, per 1000 atoms: 0.78
  Number of scatterers: 8177
  At special positions: 0
  Unit cell: (88.1309, 144.873, 96.5818, 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      49     16.00
     O    1495      8.00
     N    1435      7.00
     C    5198      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 188 " - pdb=" SG  CYS R 258 " 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: 1.99
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      41.5% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.766A  pdb=" N   GLN A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.624A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.517A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
      removed outlier: 3.503A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.517A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 22
      removed outlier: 4.217A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.856A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.697A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.685A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 144
      removed outlier: 3.820A  pdb=" N   HIS R 117 " --> pdb=" O   LYS R 113 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE R 121 " --> pdb=" O   HIS R 117 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE R 129 " --> pdb=" O   LEU R 125 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE R 141 " --> pdb=" O   ALA R 137 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LEU R 142 " --> pdb=" O   PHE R 138 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU R 144 " --> pdb=" O   LEU R 140 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 149 through 175
    Processing helix  chain 'R' and resid 177 through 184
      removed outlier: 3.586A  pdb=" N   GLN R 182 " --> pdb=" O   PRO R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 207
      removed outlier: 3.539A  pdb=" N   VAL R 191 " --> pdb=" O   TRP R 187 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE R 203 " --> pdb=" O   HIS R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 207 through 219
    Processing helix  chain 'R' and resid 227 through 236
      removed outlier: 3.909A  pdb=" N   PHE R 231 " --> pdb=" O   ARG R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 253
      removed outlier: 3.797A  pdb=" N   ILE R 242 " --> pdb=" O   VAL R 238 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 260
    Processing helix  chain 'R' and resid 269 through 302
      Proline residue:  R 275  - end of helix
      removed outlier: 3.585A  pdb=" N   ALA R 300 " --> pdb=" O   THR R 296 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER R 301 " --> pdb=" O   LYS R 297 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 319
      removed outlier: 3.545A  pdb=" N   TYR R 309 " --> pdb=" O   GLU R 305 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LYS R 314 " --> pdb=" O   ARG R 310 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 319 through 324
    Processing helix  chain 'R' and resid 325 through 330
      removed outlier: 4.548A  pdb=" N   PHE R 330 " --> pdb=" O   THR R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 337 through 354
      removed outlier: 3.527A  pdb=" N   LEU R 351 " --> pdb=" O   PHE R 347 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 354 through 364
    Processing helix  chain 'R' and resid 367 through 380
    Processing helix  chain 'P' and resid 6 through 8
      No H-bonds generated for 'chain 'P' and resid 6 through 8'
    Processing helix  chain 'P' and resid 9 through 32
      removed outlier: 3.994A  pdb=" N   ARG P  23 " --> pdb=" O   LEU P  19 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA P  24 " --> pdb=" O   GLU P  20 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN P  29 " --> pdb=" O   GLU P  25 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.978A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.215A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.519A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.196A  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)
      removed outlier: 3.563A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.933A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.633A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.309A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.346A  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: 6.396A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.523A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11
      removed outlier: 3.553A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1148 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: 3.04

  Time building geometry restraints manager: 2.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2672
        1.35 -     1.47: 2098
        1.47 -     1.59: 3507
        1.59 -     1.71: 0
        1.71 -     1.84: 69
  Bond restraints: 8346
  Sorted by residual:
  bond pdb=" N   ILE B 229 "
       pdb=" CA  ILE B 229 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 1.10e-02 8.26e+03 8.43e+00
  bond pdb=" N   ILE B 273 "
       pdb=" CA  ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.15e+00
  bond pdb=" N   THR B 249 "
       pdb=" CA  THR B 249 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.18e-02 7.18e+03 6.97e+00
  bond pdb=" N   HIS B 225 "
       pdb=" CA  HIS B 225 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 6.94e+00
  bond pdb=" N   SER B 245 "
       pdb=" CA  SER B 245 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.031 1.29e-02 6.01e+03 5.96e+00
  ... (remaining 8341 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 10635
        1.08 -     2.15: 551
        2.15 -     3.23: 93
        3.23 -     4.30: 19
        4.30 -     5.38: 7
  Bond angle restraints: 11305
  Sorted by residual:
  angle pdb=" N   ASP B 246 "
        pdb=" CA  ASP B 246 "
        pdb=" C   ASP B 246 "
      ideal   model   delta    sigma   weight residual
     113.01  109.19    3.82 1.20e+00 6.94e-01 1.01e+01
  angle pdb=" N   ASP B 247 "
        pdb=" CA  ASP B 247 "
        pdb=" C   ASP B 247 "
      ideal   model   delta    sigma   weight residual
     113.01  109.31    3.70 1.20e+00 6.94e-01 9.53e+00
  angle pdb=" CA  GLY B 272 "
        pdb=" C   GLY B 272 "
        pdb=" O   GLY B 272 "
      ideal   model   delta    sigma   weight residual
     122.31  118.24    4.07 1.34e+00 5.57e-01 9.21e+00
  angle pdb=" N   VAL R 313 "
        pdb=" CA  VAL R 313 "
        pdb=" C   VAL R 313 "
      ideal   model   delta    sigma   weight residual
     111.58  108.38    3.20 1.06e+00 8.90e-01 9.13e+00
  angle pdb=" CA  ASP B 228 "
        pdb=" C   ASP B 228 "
        pdb=" O   ASP B 228 "
      ideal   model   delta    sigma   weight residual
     121.19  118.07    3.12 1.10e+00 8.26e-01 8.03e+00
  ... (remaining 11300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 4522
       17.23 -    34.47: 339
       34.47 -    51.70: 54
       51.70 -    68.93: 8
       68.93 -    86.17: 8
  Dihedral angle restraints: 4931
    sinusoidal: 1970
      harmonic: 2961
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.17  -86.17     1      1.00e+01 1.00e-02 8.96e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.54  -29.46     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  HIS B 142 "
           pdb=" C   HIS B 142 "
           pdb=" N   THR B 143 "
           pdb=" CA  THR B 143 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.84   21.16     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 4928 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 888
       0.040 -    0.079: 266
       0.079 -    0.119: 79
       0.119 -    0.159: 10
       0.159 -    0.198: 3
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.81e-01
  chirality pdb=" CA  ASP B 228 "
            pdb=" N   ASP B 228 "
            pdb=" C   ASP B 228 "
            pdb=" CB  ASP B 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CA  ILE B 229 "
            pdb=" N   ILE B 229 "
            pdb=" C   ILE B 229 "
            pdb=" CB  ILE B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.49e-01
  ... (remaining 1243 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 238 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO R 239 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO R 239 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 239 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B 236 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.011 2.00e-02 2.50e+03   1.03e-02 2.12e+00
        pdb=" CG  TYR B  59 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 955
        2.75 -     3.29: 7757
        3.29 -     3.82: 13342
        3.82 -     4.36: 17688
        4.36 -     4.90: 29567
  Nonbonded interactions: 69309
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   SER R 349 "
            pdb=" OG  SER R 353 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ASP R 224 "
            pdb=" NH1 ARG R 227 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OE2 GLU R 352 "
            pdb=" O   HOH R 501 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.263 3.040
  ... (remaining 69304 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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.350
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:28.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8349  Z= 0.185
  Angle     :  0.569   5.379  11311  Z= 0.360
  Chirality :  0.042   0.198   1246
  Planarity :  0.003   0.041   1443
  Dihedral  : 12.458  79.634   3008
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.48 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.97 (0.22), residues: 1001
  helix: -3.96 (0.14), residues: 390
  sheet: -1.21 (0.33), residues: 219
  loop : -1.72 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  99 
 HIS   0.007   0.001   HIS B  62 
 PHE   0.015   0.001   PHE N 108 
 TYR   0.025   0.001   TYR B  59 
 ARG   0.002   0.000   ARG N 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28423 (  397)
  hydrogen bonds       : angle      10.47940 ( 1148)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       1.51010 (    6)
  covalent geometry    : bond        0.00351 ( 8346)
  covalent geometry    : angle       0.56771 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A  209 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6481 (mt-10)
REVERT: A  220 HIS cc_start: 0.7940 (t-170) cc_final: 0.7686 (t70)
REVERT: A  280 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8360 (ptpt)
REVERT: A  283 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7089 (mtt-85)
REVERT: A  339 TYR cc_start: 0.8360 (m-80) cc_final: 0.7784 (m-80)
REVERT: A  344 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7943 (mm-30)
REVERT: B   23 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7860 (tppt)
REVERT: B   46 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7071 (mmm-85)
REVERT: B   76 ASP cc_start: 0.8810 (p0) cc_final: 0.8440 (p0)
REVERT: B  138 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7607 (mt-10)
REVERT: B  245 SER cc_start: 0.9034 (t) cc_final: 0.8735 (t)
REVERT: B  246 ASP cc_start: 0.8221 (m-30) cc_final: 0.7968 (m-30)
REVERT: B  312 ASP cc_start: 0.7919 (m-30) cc_final: 0.7714 (m-30)
REVERT: G   20 LYS cc_start: 0.8080 (mttm) cc_final: 0.7704 (mtmm)
REVERT: G   32 LYS cc_start: 0.8608 (tmtt) cc_final: 0.8228 (tptm)
REVERT: N    5 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7492 (mm110)
REVERT: N   34 MET cc_start: 0.8941 (mmm) cc_final: 0.8444 (mmm)
REVERT: N   83 MET cc_start: 0.9050 (mtp) cc_final: 0.8422 (mtp)
REVERT: R  225 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7292 (mtp180)
REVERT: R  234 ILE cc_start: 0.8596 (mt) cc_final: 0.8385 (mm)
REVERT: R  333 ASN cc_start: 0.7704 (t0) cc_final: 0.7434 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 153
  average time/residue: 1.3764
  time to fit residues: 221.9014
Evaluate side-chains
  116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0370
   chunk 89 optimal weight:    6.9990
   overall best weight:    2.0066

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 218 ASN
A 264 ASN
A 279 ASN
A 377 ASN
B  75 GLN
B 110 ASN
B 119 ASN
B 155 ASN
G  18 GLN
R 127 HIS
R 166 ASN
R 173 GLN
R 182 GLN
R 379 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.130971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.097701 restraints weight = 26449.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 3.65
r_work: 0.2734 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8349  Z= 0.204
  Angle     :  0.620  15.470  11311  Z= 0.326
  Chirality :  0.045   0.159   1246
  Planarity :  0.005   0.048   1443
  Dihedral  :  4.798  27.791   1119
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  8.54 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.24), residues: 1001
  helix: -1.45 (0.23), residues: 400
  sheet: -0.63 (0.34), residues: 227
  loop : -1.28 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 339 
 HIS   0.010   0.002   HIS A 357 
 PHE   0.020   0.002   PHE N 108 
 TYR   0.016   0.002   TYR B 105 
 ARG   0.011   0.001   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05512 (  397)
  hydrogen bonds       : angle       5.58059 ( 1148)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       1.90572 (    6)
  covalent geometry    : bond        0.00481 ( 8346)
  covalent geometry    : angle       0.61843 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.426 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7367 (tt0) cc_final: 0.7117 (tt0)
REVERT: A   25 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7810 (tttp)
REVERT: A  280 LYS cc_start: 0.8872 (ptmt) cc_final: 0.8652 (ptpt)
REVERT: A  283 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7693 (mtt-85)
REVERT: A  284 ASP cc_start: 0.8784 (m-30) cc_final: 0.8545 (m-30)
REVERT: A  389 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7378 (mtp180)
REVERT: B   13 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7366 (tt0)
REVERT: B   23 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7980 (tppt)
REVERT: B   46 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7380 (mmm-85)
REVERT: B   76 ASP cc_start: 0.9124 (p0) cc_final: 0.8720 (p0)
REVERT: B  134 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6957 (mmp80)
REVERT: B  153 ASP cc_start: 0.8730 (m-30) cc_final: 0.8372 (m-30)
REVERT: B  217 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8658 (pmt)
REVERT: B  262 MET cc_start: 0.9174 (ttm) cc_final: 0.8940 (tpp)
REVERT: G   20 LYS cc_start: 0.8042 (mttm) cc_final: 0.7775 (mtmm)
REVERT: G   32 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8550 (tptm)
REVERT: N    5 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7585 (mm110)
REVERT: N   19 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8260 (ttt180)
REVERT: N   34 MET cc_start: 0.9213 (mmm) cc_final: 0.8630 (mmm)
REVERT: N   52 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8344 (p)
REVERT: N   83 MET cc_start: 0.9226 (mtp) cc_final: 0.8859 (mtp)
REVERT: N   89 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7415 (pm20)
REVERT: R  206 MET cc_start: 0.8935 (mtm) cc_final: 0.8595 (mtm)
REVERT: R  333 ASN cc_start: 0.7925 (t0) cc_final: 0.7552 (t0)
REVERT: P   21 MET cc_start: 0.7574 (ttm) cc_final: 0.7222 (ttp)
  outliers start: 19
  outliers final: 8
  residues processed: 138
  average time/residue: 2.0128
  time to fit residues: 292.7371
Evaluate side-chains
  126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 1.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0980
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B 142 HIS
B 155 ASN
R 182 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.132693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.099945 restraints weight = 17380.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.49
r_work: 0.2821 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8349  Z= 0.141
  Angle     :  0.539  14.096  11311  Z= 0.283
  Chirality :  0.043   0.137   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.573  25.559   1119
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.39 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.87 (0.26), residues: 1001
  helix: -0.18 (0.25), residues: 400
  sheet: -0.35 (0.33), residues: 227
  loop : -0.97 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 260 
 TYR   0.011   0.001   TYR R 363 
 ARG   0.011   0.000   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (  397)
  hydrogen bonds       : angle       4.95499 ( 1148)
  SS BOND              : bond        0.00181 (    3)
  SS BOND              : angle       1.44950 (    6)
  covalent geometry    : bond        0.00322 ( 8346)
  covalent geometry    : angle       0.53855 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 1.506 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7294 (tt0) cc_final: 0.7077 (tt0)
REVERT: A   20 ARG cc_start: 0.7540 (mtm110) cc_final: 0.7221 (mtm110)
REVERT: A   25 LYS cc_start: 0.8389 (ttmm) cc_final: 0.7800 (tttp)
REVERT: A  264 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7099 (p0)
REVERT: A  284 ASP cc_start: 0.8634 (m-30) cc_final: 0.8397 (m-30)
REVERT: A  389 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7435 (mtp180)
REVERT: B   23 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8000 (tppt)
REVERT: B   46 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7377 (mmm-85)
REVERT: B   76 ASP cc_start: 0.9017 (p0) cc_final: 0.8677 (p0)
REVERT: B  134 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6934 (mmp80)
REVERT: B  217 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8616 (pmt)
REVERT: G   20 LYS cc_start: 0.8055 (mttm) cc_final: 0.7821 (mtmm)
REVERT: G   21 MET cc_start: 0.7176 (mmm) cc_final: 0.6941 (ptm)
REVERT: G   32 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8513 (tptm)
REVERT: N    5 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7440 (mm110)
REVERT: N   19 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8248 (ttt180)
REVERT: N   34 MET cc_start: 0.9153 (mmm) cc_final: 0.8683 (mmm)
REVERT: R  206 MET cc_start: 0.8953 (mtm) cc_final: 0.8580 (mtm)
REVERT: R  333 ASN cc_start: 0.7831 (t0) cc_final: 0.7539 (t0)
REVERT: P   21 MET cc_start: 0.7574 (ttm) cc_final: 0.7213 (ttp)
  outliers start: 17
  outliers final: 5
  residues processed: 141
  average time/residue: 1.5437
  time to fit residues: 228.9651
Evaluate side-chains
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B 155 ASN
R 173 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.133125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.098995 restraints weight = 16119.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.44
r_work: 0.2790 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8349  Z= 0.160
  Angle     :  0.556  15.610  11311  Z= 0.288
  Chirality :  0.044   0.139   1246
  Planarity :  0.004   0.047   1443
  Dihedral  :  4.604  25.607   1119
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.21 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.26), residues: 1001
  helix:  0.36 (0.26), residues: 400
  sheet: -0.24 (0.33), residues: 232
  loop : -0.82 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N  47 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.016   0.002   PHE R 260 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.011   0.001   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04272 (  397)
  hydrogen bonds       : angle       4.76736 ( 1148)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       1.61495 (    6)
  covalent geometry    : bond        0.00376 ( 8346)
  covalent geometry    : angle       0.55475 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7311 (tt0) cc_final: 0.7049 (tt0)
REVERT: A   20 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7272 (mtm110)
REVERT: A   25 LYS cc_start: 0.8415 (ttmm) cc_final: 0.7845 (tttp)
REVERT: A  389 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7383 (mtp180)
REVERT: B   23 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8018 (tppt)
REVERT: B   46 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7418 (mmt-90)
REVERT: B   76 ASP cc_start: 0.9023 (p0) cc_final: 0.8646 (p0)
REVERT: B   86 THR cc_start: 0.8853 (m) cc_final: 0.8572 (p)
REVERT: B  134 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6913 (mmp80)
REVERT: B  217 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8702 (pmt)
REVERT: G   20 LYS cc_start: 0.8073 (mttm) cc_final: 0.7825 (mtmm)
REVERT: G   21 MET cc_start: 0.7220 (mmm) cc_final: 0.6954 (ptm)
REVERT: G   32 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8462 (tptm)
REVERT: N    5 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7510 (mm110)
REVERT: N   19 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8233 (ttt180)
REVERT: N   34 MET cc_start: 0.9192 (mmm) cc_final: 0.8720 (mmm)
REVERT: N   89 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7230 (pm20)
REVERT: R  206 MET cc_start: 0.8971 (mtm) cc_final: 0.8585 (mtm)
REVERT: R  333 ASN cc_start: 0.7912 (t0) cc_final: 0.7621 (t0)
REVERT: P   21 MET cc_start: 0.7655 (ttm) cc_final: 0.7275 (ttp)
  outliers start: 22
  outliers final: 11
  residues processed: 131
  average time/residue: 1.4615
  time to fit residues: 201.4683
Evaluate side-chains
  132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
B 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.133470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.100931 restraints weight = 17735.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.62
r_work: 0.2819 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8349  Z= 0.150
  Angle     :  0.539  14.614  11311  Z= 0.280
  Chirality :  0.043   0.136   1246
  Planarity :  0.004   0.047   1443
  Dihedral  :  4.545  24.570   1119
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.78 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.26), residues: 1001
  helix:  0.63 (0.26), residues: 400
  sheet: -0.09 (0.33), residues: 226
  loop : -0.78 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N  47 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.016   0.001   PHE R 260 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.011   0.000   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  397)
  hydrogen bonds       : angle       4.63747 ( 1148)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       1.47579 (    6)
  covalent geometry    : bond        0.00350 ( 8346)
  covalent geometry    : angle       0.53768 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7329 (tt0) cc_final: 0.7066 (tt0)
REVERT: A   20 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7259 (mtm110)
REVERT: A   25 LYS cc_start: 0.8399 (ttmm) cc_final: 0.7841 (tttp)
REVERT: A  389 ARG cc_start: 0.7833 (ttp-110) cc_final: 0.7386 (mtp180)
REVERT: B   23 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8064 (tppt)
REVERT: B   46 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7447 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8995 (p0) cc_final: 0.8598 (p0)
REVERT: B   86 THR cc_start: 0.8732 (m) cc_final: 0.8510 (p)
REVERT: B  134 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6886 (mmp80)
REVERT: B  217 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8793 (pmt)
REVERT: B  291 ASP cc_start: 0.8042 (p0) cc_final: 0.7750 (p0)
REVERT: B  312 ASP cc_start: 0.8400 (m-30) cc_final: 0.8159 (m-30)
REVERT: G   20 LYS cc_start: 0.8129 (mttm) cc_final: 0.7872 (mtmm)
REVERT: G   21 MET cc_start: 0.7174 (mmm) cc_final: 0.6862 (ptm)
REVERT: G   32 LYS cc_start: 0.8725 (tmtt) cc_final: 0.8392 (tptm)
REVERT: N    5 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7463 (mm110)
REVERT: N   19 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8242 (ttt180)
REVERT: N   34 MET cc_start: 0.9177 (mmm) cc_final: 0.8701 (mmm)
REVERT: N   89 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7349 (pm20)
REVERT: R  206 MET cc_start: 0.8966 (mtm) cc_final: 0.8589 (mtm)
REVERT: R  333 ASN cc_start: 0.7920 (t0) cc_final: 0.7615 (t0)
  outliers start: 26
  outliers final: 10
  residues processed: 130
  average time/residue: 1.4344
  time to fit residues: 196.3170
Evaluate side-chains
  126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0570
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    0.3980
   chunk 12 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0770
   chunk 24 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 155 ASN
B 340 ASN
G  59 ASN
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.135142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.103148 restraints weight = 17067.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.44
r_work: 0.2866 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8349  Z= 0.103
  Angle     :  0.484  11.415  11311  Z= 0.255
  Chirality :  0.041   0.135   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.256  21.338   1119
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.12 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1001
  helix:  0.99 (0.26), residues: 400
  sheet: -0.04 (0.33), residues: 228
  loop : -0.63 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.012   0.000   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  397)
  hydrogen bonds       : angle       4.33038 ( 1148)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       1.06507 (    6)
  covalent geometry    : bond        0.00223 ( 8346)
  covalent geometry    : angle       0.48381 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7285 (tt0) cc_final: 0.6993 (tt0)
REVERT: A   20 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7129 (mtm110)
REVERT: A   25 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7777 (tttp)
REVERT: A  389 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7456 (mtp180)
REVERT: B   23 LYS cc_start: 0.8294 (ttpp) cc_final: 0.8019 (tppt)
REVERT: B   46 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7472 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8925 (p0) cc_final: 0.8534 (p0)
REVERT: B  134 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6898 (mmp80)
REVERT: B  217 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8744 (pmt)
REVERT: B  246 ASP cc_start: 0.8649 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  291 ASP cc_start: 0.7940 (p0) cc_final: 0.7633 (p0)
REVERT: B  312 ASP cc_start: 0.8294 (m-30) cc_final: 0.8022 (m-30)
REVERT: G   20 LYS cc_start: 0.8076 (mttm) cc_final: 0.7686 (mtmm)
REVERT: G   21 MET cc_start: 0.7033 (mmm) cc_final: 0.6773 (ptm)
REVERT: G   32 LYS cc_start: 0.8648 (tmtt) cc_final: 0.8349 (tptm)
REVERT: N    5 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7428 (mm110)
REVERT: N   19 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8229 (ttt180)
REVERT: N   34 MET cc_start: 0.9158 (mmm) cc_final: 0.8623 (mmm)
REVERT: N   87 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7637 (ptpp)
REVERT: N   89 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7101 (pm20)
REVERT: R  262 LYS cc_start: 0.8384 (tttt) cc_final: 0.8103 (tttp)
REVERT: R  333 ASN cc_start: 0.7858 (t0) cc_final: 0.7574 (t0)
  outliers start: 24
  outliers final: 12
  residues processed: 131
  average time/residue: 1.4293
  time to fit residues: 197.3459
Evaluate side-chains
  126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 220 GLN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.129290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.096650 restraints weight = 17543.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.51
r_work: 0.2759 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   8349  Z= 0.249
  Angle     :  0.629  18.112  11311  Z= 0.324
  Chirality :  0.047   0.158   1246
  Planarity :  0.005   0.045   1443
  Dihedral  :  4.815  25.811   1119
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.01 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1001
  helix:  0.70 (0.26), residues: 400
  sheet: -0.05 (0.34), residues: 230
  loop : -0.65 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP N  47 
 HIS   0.012   0.002   HIS A 220 
 PHE   0.023   0.002   PHE N 108 
 TYR   0.014   0.002   TYR R 212 
 ARG   0.011   0.001   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04594 (  397)
  hydrogen bonds       : angle       4.74824 ( 1148)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       2.04383 (    6)
  covalent geometry    : bond        0.00605 ( 8346)
  covalent geometry    : angle       0.62747 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7427 (tt0) cc_final: 0.7040 (tp30)
REVERT: A   20 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7207 (mtm110)
REVERT: A   25 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7840 (tttp)
REVERT: A  389 ARG cc_start: 0.7861 (ttp-110) cc_final: 0.7391 (mtp180)
REVERT: B   13 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7554 (tp40)
REVERT: B   23 LYS cc_start: 0.8312 (ttpp) cc_final: 0.8021 (tppt)
REVERT: B   42 ARG cc_start: 0.6457 (tpt170) cc_final: 0.5914 (tpt170)
REVERT: B   46 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7420 (mmt-90)
REVERT: B   76 ASP cc_start: 0.9004 (p0) cc_final: 0.8582 (p0)
REVERT: B  134 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6916 (mmp80)
REVERT: B  217 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8720 (pmt)
REVERT: B  291 ASP cc_start: 0.8075 (p0) cc_final: 0.7776 (p0)
REVERT: G   20 LYS cc_start: 0.8005 (mttm) cc_final: 0.7643 (mtmm)
REVERT: G   21 MET cc_start: 0.7095 (mmm) cc_final: 0.6788 (ptm)
REVERT: G   32 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8497 (tptm)
REVERT: N    5 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7495 (mm110)
REVERT: N   19 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8277 (ttt180)
REVERT: N   34 MET cc_start: 0.9176 (mmm) cc_final: 0.8733 (mmm)
REVERT: N   76 LYS cc_start: 0.8774 (ptpt) cc_final: 0.8561 (ptpt)
REVERT: N   80 TYR cc_start: 0.8963 (m-80) cc_final: 0.8760 (m-80)
REVERT: N   89 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7312 (pm20)
REVERT: R  333 ASN cc_start: 0.8023 (t0) cc_final: 0.7670 (t0)
  outliers start: 25
  outliers final: 13
  residues processed: 127
  average time/residue: 1.4620
  time to fit residues: 195.4600
Evaluate side-chains
  129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.131338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.098192 restraints weight = 22532.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 3.23
r_work: 0.2782 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8349  Z= 0.159
  Angle     :  0.550  15.113  11311  Z= 0.286
  Chirality :  0.044   0.138   1246
  Planarity :  0.004   0.044   1443
  Dihedral  :  4.629  24.935   1119
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.46 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1001
  helix:  0.95 (0.26), residues: 395
  sheet: -0.03 (0.34), residues: 228
  loop : -0.58 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N  47 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.017   0.002   PHE R 260 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.011   0.000   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  397)
  hydrogen bonds       : angle       4.56934 ( 1148)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       1.50764 (    6)
  covalent geometry    : bond        0.00374 ( 8346)
  covalent geometry    : angle       0.54896 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7280 (tt0) cc_final: 0.6823 (tp30)
REVERT: A   20 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7159 (mtm110)
REVERT: A   25 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7881 (tttp)
REVERT: A  389 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7384 (mtp180)
REVERT: B   13 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7576 (tp40)
REVERT: B   23 LYS cc_start: 0.8348 (ttpp) cc_final: 0.8051 (tppt)
REVERT: B   46 ARG cc_start: 0.8188 (mtm180) cc_final: 0.7413 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8976 (p0) cc_final: 0.8556 (p0)
REVERT: B  134 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6904 (mmp80)
REVERT: B  217 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8680 (pmt)
REVERT: B  291 ASP cc_start: 0.8004 (p0) cc_final: 0.7709 (p0)
REVERT: B  312 ASP cc_start: 0.8405 (m-30) cc_final: 0.8147 (m-30)
REVERT: G   20 LYS cc_start: 0.7989 (mttm) cc_final: 0.7591 (mtmm)
REVERT: G   32 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8336 (tptm)
REVERT: N    5 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7505 (mm110)
REVERT: N   19 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8222 (ttt180)
REVERT: N   34 MET cc_start: 0.9181 (mmm) cc_final: 0.8752 (mmm)
REVERT: N   87 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7662 (ptpp)
REVERT: N   89 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7365 (pm20)
REVERT: R  333 ASN cc_start: 0.7878 (t0) cc_final: 0.7524 (t0)
  outliers start: 25
  outliers final: 14
  residues processed: 127
  average time/residue: 1.4250
  time to fit residues: 190.7456
Evaluate side-chains
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 88 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 268 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.133572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.100280 restraints weight = 23546.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.33
r_work: 0.2810 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8349  Z= 0.115
  Angle     :  0.505  12.680  11311  Z= 0.265
  Chirality :  0.042   0.140   1246
  Planarity :  0.004   0.045   1443
  Dihedral  :  4.385  22.528   1119
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.01 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.27), residues: 1001
  helix:  1.20 (0.26), residues: 395
  sheet:  0.11 (0.34), residues: 219
  loop : -0.48 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.011   0.000   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03656 (  397)
  hydrogen bonds       : angle       4.36858 ( 1148)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       1.27305 (    6)
  covalent geometry    : bond        0.00259 ( 8346)
  covalent geometry    : angle       0.50460 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7308 (tt0) cc_final: 0.6889 (tp30)
REVERT: A   20 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7155 (mtm110)
REVERT: A   25 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7826 (tttp)
REVERT: A  308 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7159 (mm)
REVERT: A  389 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7425 (mtp180)
REVERT: B   13 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7594 (tp-100)
REVERT: B   23 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8090 (tppt)
REVERT: B   46 ARG cc_start: 0.8230 (mtm180) cc_final: 0.7389 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8949 (p0) cc_final: 0.8527 (p0)
REVERT: B  134 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6919 (mmp80)
REVERT: B  217 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8704 (pmt)
REVERT: B  291 ASP cc_start: 0.7942 (p0) cc_final: 0.7640 (p0)
REVERT: B  312 ASP cc_start: 0.8389 (m-30) cc_final: 0.8125 (m-30)
REVERT: G   20 LYS cc_start: 0.8043 (mttm) cc_final: 0.7657 (mtmm)
REVERT: G   32 LYS cc_start: 0.8616 (tmtt) cc_final: 0.8301 (tptm)
REVERT: N    5 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7443 (mm110)
REVERT: N   19 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8233 (ttt180)
REVERT: N   34 MET cc_start: 0.9179 (mmm) cc_final: 0.8710 (mmm)
REVERT: N   87 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7595 (ptpp)
REVERT: N   89 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7399 (pm20)
REVERT: R  333 ASN cc_start: 0.7873 (t0) cc_final: 0.7526 (t0)
  outliers start: 27
  outliers final: 14
  residues processed: 119
  average time/residue: 1.4149
  time to fit residues: 177.4221
Evaluate side-chains
  123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
B 268 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.132587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.099322 restraints weight = 16787.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.46
r_work: 0.2805 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2794
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2794
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8349  Z= 0.142
  Angle     :  0.534  13.885  11311  Z= 0.278
  Chirality :  0.043   0.138   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.451  22.741   1119
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.35 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1001
  helix:  1.22 (0.26), residues: 395
  sheet:  0.16 (0.35), residues: 219
  loop : -0.48 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N  47 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.011   0.000   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  397)
  hydrogen bonds       : angle       4.41876 ( 1148)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       1.50087 (    6)
  covalent geometry    : bond        0.00332 ( 8346)
  covalent geometry    : angle       0.53311 (11305)

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7414 (tt0) cc_final: 0.7161 (tt0)
REVERT: A   20 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7292 (mtm110)
REVERT: A   25 LYS cc_start: 0.8383 (ttmm) cc_final: 0.7881 (tttp)
REVERT: A  389 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7381 (mtp180)
REVERT: B   13 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7547 (tp-100)
REVERT: B   23 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8097 (tppt)
REVERT: B   46 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7464 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8949 (p0) cc_final: 0.8544 (p0)
REVERT: B  134 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6907 (mmp80)
REVERT: B  217 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8695 (pmt)
REVERT: B  268 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7854 (m110)
REVERT: B  291 ASP cc_start: 0.8009 (p0) cc_final: 0.7692 (p0)
REVERT: B  312 ASP cc_start: 0.8388 (m-30) cc_final: 0.8123 (m-30)
REVERT: G   20 LYS cc_start: 0.8003 (mttm) cc_final: 0.7612 (mtmm)
REVERT: N    5 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7483 (mm110)
REVERT: N   19 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8281 (ttt180)
REVERT: N   34 MET cc_start: 0.9179 (mmm) cc_final: 0.8693 (mmm)
REVERT: N   87 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7638 (ptpp)
REVERT: N   89 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7410 (pm20)
REVERT: R  206 MET cc_start: 0.8378 (mtp) cc_final: 0.8163 (ttm)
REVERT: R  333 ASN cc_start: 0.7902 (t0) cc_final: 0.7550 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 121
  average time/residue: 1.4528
  time to fit residues: 184.9030
Evaluate side-chains
  132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
B 155 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.134593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.101341 restraints weight = 19714.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.88
r_work: 0.2827 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8349  Z= 0.117
  Angle     :  0.508  12.552  11311  Z= 0.267
  Chirality :  0.042   0.140   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.375  22.145   1119
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.12 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.27), residues: 1001
  helix:  1.34 (0.26), residues: 395
  sheet:  0.20 (0.34), residues: 219
  loop : -0.48 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.011   0.000   ARG R 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03660 (  397)
  hydrogen bonds       : angle       4.33791 ( 1148)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       1.32038 (    6)
  covalent geometry    : bond        0.00265 ( 8346)
  covalent geometry    : angle       0.50704 (11305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6789.97 seconds
wall clock time: 118 minutes 33.26 seconds (7113.26 seconds total)