Starting phenix.real_space_refine
on Tue Mar  3 18:36:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p9x_20277/03_2026/6p9x_20277.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p9x_20277/03_2026/6p9x_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p9x_20277/03_2026/6p9x_20277.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p9x_20277/03_2026/6p9x_20277.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p9x_20277/03_2026/6p9x_20277.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p9x_20277/03_2026/6p9x_20277.map"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.50, per 1000 atoms: 0.31
  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: 0.46
  Conformation dependent library (CDL) restraints added in 455.2 milliseconds
  

  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: 0.28
  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: 1.24

  Time building geometry restraints manager: 0.62 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.160
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.040
-------------------------------------------------------------------------------
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 : 5.52
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG N 118 
 TYR   0.025   0.001   TYR B  59 
 PHE   0.015   0.001   PHE N 108 
 TRP   0.010   0.001   TRP B  99 
 HIS   0.007   0.001   HIS B  62 

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

*********************** 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  : 0.324 
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: 0.8439 (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: 0.7969 (m-30)
REVERT: B  312 ASP cc_start: 0.7919 (m-30) cc_final: 0.7713 (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: 0.7491 (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: 0.6571
  time to fit residues: 105.6856
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  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.131724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.099722 restraints weight = 21460.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 3.11
r_work: 0.2801 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    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 = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1628

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= 0.178
  Angle     :  0.596  14.077  11311  Z= 0.315
  Chirality :  0.045   0.164   1246
  Planarity :  0.005   0.048   1443
  Dihedral  :  4.698  26.532   1119
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  8.54 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.24), residues: 1001
  helix: -1.41 (0.23), residues: 398
  sheet: -0.62 (0.34), residues: 227
  loop : -1.28 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 310 
 TYR   0.016   0.002   TYR B 105 
 PHE   0.018   0.002   PHE N 108 
 TRP   0.016   0.002   TRP B 339 
 HIS   0.009   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8346)
  covalent geometry    : angle       0.59464 (11305)
  SS BOND              : bond        0.00236 (    3)
  SS BOND              : angle       1.75716 (    6)
  hydrogen bonds       : bond        0.05361 (  397)
  hydrogen bonds       : angle       5.52585 ( 1148)

*********************** 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
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7335 (tt0) cc_final: 0.7127 (tt0)
REVERT: A   25 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7831 (tttp)
REVERT: A  280 LYS cc_start: 0.8877 (ptmt) cc_final: 0.8650 (ptpt)
REVERT: A  283 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7702 (mtt-85)
REVERT: A  284 ASP cc_start: 0.8703 (m-30) cc_final: 0.8461 (m-30)
REVERT: A  389 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7373 (mtp180)
REVERT: B   13 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7380 (tt0)
REVERT: B   23 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8017 (tppt)
REVERT: B   46 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7425 (mmm-85)
REVERT: B   76 ASP cc_start: 0.9092 (p0) cc_final: 0.8710 (p0)
REVERT: B  134 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6934 (mmp80)
REVERT: B  217 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8697 (pmt)
REVERT: B  262 MET cc_start: 0.9124 (ttm) cc_final: 0.8892 (tpp)
REVERT: G   20 LYS cc_start: 0.8107 (mttm) cc_final: 0.7880 (mtmm)
REVERT: G   21 MET cc_start: 0.7227 (mmm) cc_final: 0.6997 (ptm)
REVERT: G   32 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8545 (tptm)
REVERT: N    5 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7594 (mm110)
REVERT: N   19 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8263 (ttt180)
REVERT: N   34 MET cc_start: 0.9161 (mmm) cc_final: 0.8730 (mmm)
REVERT: N   52 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8387 (p)
REVERT: N   83 MET cc_start: 0.9215 (mtp) cc_final: 0.8876 (mtp)
REVERT: N   89 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7520 (pm20)
REVERT: R  206 MET cc_start: 0.8915 (mtm) cc_final: 0.8573 (mtm)
REVERT: R  333 ASN cc_start: 0.7870 (t0) cc_final: 0.7507 (t0)
REVERT: P   21 MET cc_start: 0.7574 (ttm) cc_final: 0.7223 (ttp)
  outliers start: 18
  outliers final: 7
  residues processed: 141
  average time/residue: 0.6754
  time to fit residues: 99.9863
Evaluate side-chains
  127 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  270 ILE
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 48 optimal weight:    0.6980
   chunk 32 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.135179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.100982 restraints weight = 20649.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.05
r_work: 0.2803 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    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 = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8349  Z= 0.132
  Angle     :  0.529  13.111  11311  Z= 0.278
  Chirality :  0.043   0.136   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.496  24.501   1119
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.39 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.25), residues: 1001
  helix: -0.18 (0.25), residues: 400
  sheet: -0.36 (0.33), residues: 227
  loop : -0.97 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 310 
 TYR   0.011   0.001   TYR R 363 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.014   0.001   TRP B 339 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8346)
  covalent geometry    : angle       0.52842 (11305)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       1.40189 (    6)
  hydrogen bonds       : bond        0.04343 (  397)
  hydrogen bonds       : angle       4.92967 ( 1148)

*********************** 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
  145 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7306 (tt0) cc_final: 0.7069 (tt0)
REVERT: A   20 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7180 (mtm110)
REVERT: A   25 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7736 (tttp)
REVERT: A  264 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.6920 (p0)
REVERT: A  283 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7581 (mtt-85)
REVERT: A  284 ASP cc_start: 0.8663 (m-30) cc_final: 0.8426 (m-30)
REVERT: A  389 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7396 (mtp180)
REVERT: B   23 LYS cc_start: 0.8318 (ttpp) cc_final: 0.7957 (tppt)
REVERT: B   46 ARG cc_start: 0.8197 (mtm180) cc_final: 0.7311 (mmm-85)
REVERT: B   76 ASP cc_start: 0.9018 (p0) cc_final: 0.8685 (p0)
REVERT: B  134 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6910 (mmp80)
REVERT: G   20 LYS cc_start: 0.8012 (mttm) cc_final: 0.7781 (mtmm)
REVERT: G   21 MET cc_start: 0.7170 (mmm) cc_final: 0.6928 (ptm)
REVERT: G   32 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8437 (tptm)
REVERT: N    5 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7409 (mm110)
REVERT: N   19 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8245 (ttt180)
REVERT: N   25 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8198 (p)
REVERT: N   34 MET cc_start: 0.9177 (mmm) cc_final: 0.8666 (mmm)
REVERT: R  206 MET cc_start: 0.8913 (mtm) cc_final: 0.8481 (mtm)
REVERT: R  230 MET cc_start: 0.8406 (mtt) cc_final: 0.8049 (mtp)
REVERT: R  333 ASN cc_start: 0.7817 (t0) cc_final: 0.7527 (t0)
REVERT: P   21 MET cc_start: 0.7538 (ttm) cc_final: 0.7182 (ttp)
  outliers start: 19
  outliers final: 7
  residues processed: 136
  average time/residue: 0.6829
  time to fit residues: 97.5561
Evaluate side-chains
  129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  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   25 SER
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 95 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0670
   chunk 57 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
A 387 HIS
B 340 ASN
G  59 ASN
N  31 ASN
R 173 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.135640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.102465 restraints weight = 22400.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.13
r_work: 0.2853 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    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 = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8349  Z= 0.104
  Angle     :  0.486  11.197  11311  Z= 0.257
  Chirality :  0.042   0.135   1246
  Planarity :  0.004   0.045   1443
  Dihedral  :  4.259  21.841   1119
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.21 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.26), residues: 1001
  helix:  0.47 (0.26), residues: 400
  sheet: -0.25 (0.33), residues: 228
  loop : -0.77 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG R 310 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8346)
  covalent geometry    : angle       0.48578 (11305)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       1.12199 (    6)
  hydrogen bonds       : bond        0.03776 (  397)
  hydrogen bonds       : angle       4.54759 ( 1148)

*********************** 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
  143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7317 (tt0) cc_final: 0.7063 (tt0)
REVERT: A   20 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7209 (mtm110)
REVERT: A   25 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7782 (tttp)
REVERT: A  283 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7602 (mtt-85)
REVERT: A  284 ASP cc_start: 0.8580 (m-30) cc_final: 0.8356 (m-30)
REVERT: A  389 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7433 (mtp180)
REVERT: B   23 LYS cc_start: 0.8331 (ttpp) cc_final: 0.8011 (tppt)
REVERT: B   46 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7392 (mmm-85)
REVERT: B   76 ASP cc_start: 0.9000 (p0) cc_final: 0.8659 (p0)
REVERT: B   86 THR cc_start: 0.8736 (m) cc_final: 0.8352 (p)
REVERT: B  134 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6903 (mmp80)
REVERT: B  291 ASP cc_start: 0.7935 (p0) cc_final: 0.7649 (p0)
REVERT: B  312 ASP cc_start: 0.8321 (m-30) cc_final: 0.8112 (m-30)
REVERT: G   20 LYS cc_start: 0.8140 (mttm) cc_final: 0.7906 (mtmm)
REVERT: G   21 MET cc_start: 0.7148 (mmm) cc_final: 0.6901 (ptm)
REVERT: G   32 LYS cc_start: 0.8704 (tmtt) cc_final: 0.8391 (tptm)
REVERT: N    5 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7417 (mm110)
REVERT: N   19 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8180 (ttt180)
REVERT: N   25 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8294 (p)
REVERT: N   34 MET cc_start: 0.9134 (mmm) cc_final: 0.8570 (mmm)
REVERT: N   89 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7421 (pm20)
REVERT: R  206 MET cc_start: 0.8891 (mtm) cc_final: 0.8495 (mtm)
REVERT: R  333 ASN cc_start: 0.7777 (t0) cc_final: 0.7493 (t0)
REVERT: P   21 MET cc_start: 0.7635 (ttm) cc_final: 0.7228 (ttp)
  outliers start: 19
  outliers final: 9
  residues processed: 133
  average time/residue: 0.6830
  time to fit residues: 95.3498
Evaluate side-chains
  131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 62 optimal weight:    0.1980
   chunk 89 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 21 optimal weight:    0.3980
   chunk 85 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B  17 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
G  59 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.139679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.107009 restraints weight = 17914.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.54
r_work: 0.2863 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
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: 0.8081
moved from start:          0.2341

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= 0.098
  Angle     :  0.471  10.554  11311  Z= 0.249
  Chirality :  0.041   0.134   1246
  Planarity :  0.004   0.044   1443
  Dihedral  :  4.120  19.569   1119
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.26), residues: 1001
  helix:  0.90 (0.26), residues: 400
  sheet: -0.22 (0.33), residues: 226
  loop : -0.63 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 310 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 8346)
  covalent geometry    : angle       0.47088 (11305)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       1.05786 (    6)
  hydrogen bonds       : bond        0.03571 (  397)
  hydrogen bonds       : angle       4.31706 ( 1148)

*********************** 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
  140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7272 (tt0) cc_final: 0.7015 (tt0)
REVERT: A   20 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7162 (mtm110)
REVERT: A   25 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7730 (tttp)
REVERT: A  283 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7640 (mtt-85)
REVERT: A  284 ASP cc_start: 0.8615 (m-30) cc_final: 0.8404 (m-30)
REVERT: A  389 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7445 (mtp180)
REVERT: B   23 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7997 (tppt)
REVERT: B   46 ARG cc_start: 0.8271 (mtm180) cc_final: 0.7420 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8948 (p0) cc_final: 0.8576 (p0)
REVERT: B   86 THR cc_start: 0.8608 (m) cc_final: 0.8401 (p)
REVERT: B  134 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6867 (mmp80)
REVERT: B  291 ASP cc_start: 0.7893 (p0) cc_final: 0.7599 (p0)
REVERT: B  312 ASP cc_start: 0.8258 (m-30) cc_final: 0.8002 (m-30)
REVERT: G   20 LYS cc_start: 0.8145 (mttm) cc_final: 0.7910 (mtmm)
REVERT: G   21 MET cc_start: 0.7164 (mmm) cc_final: 0.6868 (ptm)
REVERT: G   32 LYS cc_start: 0.8630 (tmtt) cc_final: 0.8384 (tptm)
REVERT: N    5 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7413 (mm110)
REVERT: N   34 MET cc_start: 0.9164 (mmm) cc_final: 0.8695 (mmm)
REVERT: N   89 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7114 (pm20)
REVERT: R  206 MET cc_start: 0.8864 (mtm) cc_final: 0.8486 (mtm)
REVERT: R  333 ASN cc_start: 0.7747 (t0) cc_final: 0.7483 (t0)
  outliers start: 20
  outliers final: 9
  residues processed: 129
  average time/residue: 0.6726
  time to fit residues: 90.9897
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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  228 ASP
Chi-restraints excluded: chain B residue  336 LEU
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 11 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B  17 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

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 = 0.135173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.101548 restraints weight = 23334.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 3.23
r_work: 0.2835 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    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 = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8349  Z= 0.117
  Angle     :  0.492  11.697  11311  Z= 0.259
  Chirality :  0.042   0.134   1246
  Planarity :  0.004   0.044   1443
  Dihedral  :  4.203  19.154   1119
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.58 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.26), residues: 1001
  helix:  1.05 (0.26), residues: 400
  sheet: -0.15 (0.34), residues: 217
  loop : -0.48 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG R 310 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8346)
  covalent geometry    : angle       0.49132 (11305)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       1.28174 (    6)
  hydrogen bonds       : bond        0.03682 (  397)
  hydrogen bonds       : angle       4.29604 ( 1148)

*********************** 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
  135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7231 (tt0) cc_final: 0.6718 (tp30)
REVERT: A   20 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7156 (mtm110)
REVERT: A   25 LYS cc_start: 0.8338 (ttmm) cc_final: 0.7801 (tttp)
REVERT: A  283 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7539 (mtt-85)
REVERT: A  389 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7459 (mtp180)
REVERT: B   23 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8022 (tppt)
REVERT: B   46 ARG cc_start: 0.8256 (mtm180) cc_final: 0.7434 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8932 (p0) cc_final: 0.8545 (p0)
REVERT: B  134 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6889 (mmp80)
REVERT: B  214 ARG cc_start: 0.7844 (mmt180) cc_final: 0.7537 (mpp-170)
REVERT: B  291 ASP cc_start: 0.7949 (p0) cc_final: 0.7649 (p0)
REVERT: B  312 ASP cc_start: 0.8270 (m-30) cc_final: 0.8009 (m-30)
REVERT: G   20 LYS cc_start: 0.8093 (mttm) cc_final: 0.7769 (mtmm)
REVERT: G   21 MET cc_start: 0.7074 (mmm) cc_final: 0.6809 (ptm)
REVERT: G   32 LYS cc_start: 0.8632 (tmtt) cc_final: 0.8332 (tptm)
REVERT: N    5 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7412 (mm110)
REVERT: N   25 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8282 (p)
REVERT: N   34 MET cc_start: 0.9183 (mmm) cc_final: 0.8711 (mmm)
REVERT: R  206 MET cc_start: 0.8879 (mtm) cc_final: 0.8497 (mtm)
REVERT: R  333 ASN cc_start: 0.7785 (t0) cc_final: 0.7491 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 127
  average time/residue: 0.6427
  time to fit residues: 85.8377
Evaluate side-chains
  122 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0020
   chunk 85 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0670
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5326

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.139884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.105745 restraints weight = 14275.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.39
r_work: 0.2894 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2526

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= 0.094
  Angle     :  0.465  10.108  11311  Z= 0.247
  Chirality :  0.041   0.134   1246
  Planarity :  0.004   0.048   1443
  Dihedral  :  4.068  18.174   1119
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.27), residues: 1001
  helix:  1.26 (0.26), residues: 400
  sheet: -0.02 (0.34), residues: 217
  loop : -0.40 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG R 310 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 8346)
  covalent geometry    : angle       0.46489 (11305)
  SS BOND              : bond        0.00236 (    3)
  SS BOND              : angle       0.94978 (    6)
  hydrogen bonds       : bond        0.03438 (  397)
  hydrogen bonds       : angle       4.13608 ( 1148)

*********************** 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
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7303 (tt0) cc_final: 0.6859 (tp30)
REVERT: A   20 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7113 (mtm110)
REVERT: A   25 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7764 (tttp)
REVERT: A  283 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7568 (mtt-85)
REVERT: A  389 ARG cc_start: 0.7767 (ttp-110) cc_final: 0.7426 (mtp180)
REVERT: B   23 LYS cc_start: 0.8263 (ttpp) cc_final: 0.8016 (tppt)
REVERT: B   46 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7455 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8888 (p0) cc_final: 0.8506 (p0)
REVERT: B  134 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6867 (mmp80)
REVERT: B  214 ARG cc_start: 0.7868 (mmt180) cc_final: 0.7553 (mpp-170)
REVERT: B  291 ASP cc_start: 0.7892 (p0) cc_final: 0.7597 (p0)
REVERT: B  312 ASP cc_start: 0.8248 (m-30) cc_final: 0.7961 (m-30)
REVERT: B  325 MET cc_start: 0.8821 (tpp) cc_final: 0.8601 (mmm)
REVERT: G   20 LYS cc_start: 0.8032 (mttm) cc_final: 0.7702 (mtmm)
REVERT: G   21 MET cc_start: 0.7073 (mmm) cc_final: 0.6803 (ptm)
REVERT: G   32 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8300 (tptm)
REVERT: N    5 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7282 (mm110)
REVERT: N   25 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8301 (p)
REVERT: R  206 MET cc_start: 0.8853 (mtm) cc_final: 0.8484 (mtm)
REVERT: R  333 ASN cc_start: 0.7778 (t0) cc_final: 0.7495 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 122
  average time/residue: 0.6401
  time to fit residues: 82.2732
Evaluate side-chains
  120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  228 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 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  177 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    0.3980
   chunk 89 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**
R 202 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.135994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.102700 restraints weight = 19756.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.79
r_work: 0.2876 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8349  Z= 0.106
  Angle     :  0.477  10.684  11311  Z= 0.252
  Chirality :  0.041   0.136   1246
  Planarity :  0.004   0.049   1443
  Dihedral  :  4.106  18.420   1119
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.92 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.27), residues: 1001
  helix:  1.30 (0.26), residues: 400
  sheet:  0.05 (0.34), residues: 216
  loop : -0.37 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG R 310 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8346)
  covalent geometry    : angle       0.47596 (11305)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       1.11898 (    6)
  hydrogen bonds       : bond        0.03504 (  397)
  hydrogen bonds       : angle       4.15063 ( 1148)

*********************** 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
  131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7325 (tt0) cc_final: 0.6880 (tp30)
REVERT: A   20 ARG cc_start: 0.7556 (mtm110) cc_final: 0.7148 (mtm110)
REVERT: A   25 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7826 (tttp)
REVERT: A  283 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7523 (mtt-85)
REVERT: A  389 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7434 (mtp180)
REVERT: B   13 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7668 (tp40)
REVERT: B   23 LYS cc_start: 0.8276 (ttpp) cc_final: 0.8018 (tppt)
REVERT: B   46 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7461 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8893 (p0) cc_final: 0.8516 (p0)
REVERT: B  134 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6837 (mmp80)
REVERT: B  214 ARG cc_start: 0.7887 (mmt180) cc_final: 0.7550 (mpp-170)
REVERT: B  217 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8258 (pmm)
REVERT: B  291 ASP cc_start: 0.7924 (p0) cc_final: 0.7632 (p0)
REVERT: B  312 ASP cc_start: 0.8259 (m-30) cc_final: 0.7970 (m-30)
REVERT: B  325 MET cc_start: 0.8807 (tpp) cc_final: 0.8593 (mmm)
REVERT: G   20 LYS cc_start: 0.8107 (mttm) cc_final: 0.7792 (mtmm)
REVERT: G   21 MET cc_start: 0.6998 (mmm) cc_final: 0.6720 (ptm)
REVERT: G   32 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8277 (tptm)
REVERT: N    5 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7303 (mm110)
REVERT: N   25 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8280 (p)
REVERT: R  206 MET cc_start: 0.8892 (mtm) cc_final: 0.8531 (mtm)
REVERT: R  333 ASN cc_start: 0.7804 (t0) cc_final: 0.7514 (t0)
  outliers start: 19
  outliers final: 11
  residues processed: 122
  average time/residue: 0.6636
  time to fit residues: 85.1294
Evaluate side-chains
  123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  228 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.135559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.101664 restraints weight = 15455.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.39
r_work: 0.2858 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    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 = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2566

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= 0.114
  Angle     :  0.486  11.025  11311  Z= 0.255
  Chirality :  0.042   0.138   1246
  Planarity :  0.004   0.050   1443
  Dihedral  :  4.144  18.287   1119
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.26 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.27), residues: 1001
  helix:  1.35 (0.26), residues: 400
  sheet:  0.05 (0.34), residues: 216
  loop : -0.36 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG R 310 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8346)
  covalent geometry    : angle       0.48501 (11305)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       1.12003 (    6)
  hydrogen bonds       : bond        0.03562 (  397)
  hydrogen bonds       : angle       4.15449 ( 1148)

*********************** 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: 19
    poor density    : 113
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7317 (tt0) cc_final: 0.6826 (tp30)
REVERT: A   20 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7161 (mtm110)
REVERT: A   25 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7859 (tttp)
REVERT: A  283 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7545 (mtt-85)
REVERT: A  389 ARG cc_start: 0.7793 (ttp-110) cc_final: 0.7464 (mtp180)
REVERT: B   23 LYS cc_start: 0.8294 (ttpp) cc_final: 0.8020 (tppt)
REVERT: B   46 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7470 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8910 (p0) cc_final: 0.8526 (p0)
REVERT: B  134 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6844 (mmp80)
REVERT: B  214 ARG cc_start: 0.8087 (mmt180) cc_final: 0.7741 (mpp-170)
REVERT: B  217 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8272 (pmm)
REVERT: B  262 MET cc_start: 0.9099 (tpt) cc_final: 0.8870 (tpp)
REVERT: B  291 ASP cc_start: 0.7943 (p0) cc_final: 0.7648 (p0)
REVERT: B  312 ASP cc_start: 0.8255 (m-30) cc_final: 0.7957 (m-30)
REVERT: B  325 MET cc_start: 0.8808 (tpp) cc_final: 0.8593 (mmm)
REVERT: G   20 LYS cc_start: 0.8024 (mttm) cc_final: 0.7694 (mtmm)
REVERT: G   21 MET cc_start: 0.6994 (mmm) cc_final: 0.6708 (ptm)
REVERT: G   32 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8297 (tptm)
REVERT: N    5 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7315 (mm110)
REVERT: N   25 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8228 (p)
REVERT: R  206 MET cc_start: 0.8940 (mtm) cc_final: 0.8577 (mtm)
REVERT: R  333 ASN cc_start: 0.7825 (t0) cc_final: 0.7532 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 121
  average time/residue: 0.6478
  time to fit residues: 82.4182
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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  270 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
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 68 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 80 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.135162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.103979 restraints weight = 19000.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.56
r_work: 0.2882 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2594

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     :  0.491  11.238  11311  Z= 0.258
  Chirality :  0.042   0.140   1246
  Planarity :  0.004   0.051   1443
  Dihedral  :  4.166  18.384   1119
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.26 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.27), residues: 1001
  helix:  1.42 (0.26), residues: 400
  sheet:  0.04 (0.34), residues: 216
  loop : -0.35 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG R 310 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.011   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8346)
  covalent geometry    : angle       0.49001 (11305)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       1.16064 (    6)
  hydrogen bonds       : bond        0.03571 (  397)
  hydrogen bonds       : angle       4.16237 ( 1148)

********************** 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
  127 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7373 (tt0) cc_final: 0.7046 (tp30)
REVERT: A   20 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7229 (mtm110)
REVERT: A   25 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7955 (tttp)
REVERT: A  283 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7636 (mtt-85)
REVERT: A  389 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7511 (mtp180)
REVERT: B   23 LYS cc_start: 0.8395 (ttpp) cc_final: 0.8132 (tppt)
REVERT: B   46 ARG cc_start: 0.8271 (mtm180) cc_final: 0.7558 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8915 (p0) cc_final: 0.8548 (p0)
REVERT: B  134 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6902 (mmp80)
REVERT: B  217 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8268 (pmm)
REVERT: B  291 ASP cc_start: 0.8019 (p0) cc_final: 0.7739 (p0)
REVERT: B  312 ASP cc_start: 0.8229 (m-30) cc_final: 0.7940 (m-30)
REVERT: G   20 LYS cc_start: 0.8156 (mttm) cc_final: 0.7834 (mtmm)
REVERT: G   32 LYS cc_start: 0.8652 (tmtt) cc_final: 0.8367 (tptm)
REVERT: N    5 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7406 (mm110)
REVERT: R  176 MET cc_start: 0.7276 (tpp) cc_final: 0.7062 (mmm)
REVERT: R  206 MET cc_start: 0.8955 (mtm) cc_final: 0.8610 (mtm)
REVERT: R  333 ASN cc_start: 0.7835 (t0) cc_final: 0.7497 (t0)
  outliers start: 18
  outliers final: 15
  residues processed: 117
  average time/residue: 0.6418
  time to fit residues: 79.0371
Evaluate side-chains
  124 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
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  270 ILE
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   25 SER
Chi-restraints excluded: chain N residue   69 THR
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 76 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.135744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.102823 restraints weight = 25550.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 3.55
r_work: 0.2822 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2620

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= 0.112
  Angle     :  0.487  11.045  11311  Z= 0.256
  Chirality :  0.042   0.137   1246
  Planarity :  0.004   0.053   1443
  Dihedral  :  4.160  18.571   1119
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.49 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.27), residues: 1001
  helix:  1.44 (0.26), residues: 400
  sheet:  0.04 (0.34), residues: 216
  loop : -0.34 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG R 310 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.011   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8346)
  covalent geometry    : angle       0.48644 (11305)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       1.10387 (    6)
  hydrogen bonds       : bond        0.03530 (  397)
  hydrogen bonds       : angle       4.14020 ( 1148)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3005.25 seconds
wall clock time: 51 minutes 49.15 seconds (3109.15 seconds total)