Starting phenix.real_space_refine
on Wed Mar 12 07:43:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlz_36409/03_2025/8jlz_36409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlz_36409/03_2025/8jlz_36409.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlz_36409/03_2025/8jlz_36409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlz_36409/03_2025/8jlz_36409.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlz_36409/03_2025/8jlz_36409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlz_36409/03_2025/8jlz_36409.cif"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     Cl      1      4.86       5
     C    4917      2.51       5
     N    1336      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7730
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1831
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 46
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "B"
      Number of atoms: 2533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2533
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 54
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "G"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 420
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          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
    Chain: "N"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 953
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 1977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 1977
          Classifications: {'peptide': 268}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 15, 'TRANS': 252}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 60
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'UQL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.58, per 1000 atoms: 0.59
  Number of scatterers: 7730
  At special positions: 0
  Unit cell: (96.05, 107.1, 116.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      56     16.00
     O    1420      8.00
     N    1336      7.00
     C    4917      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  99 " - pdb=" SG  CYS R 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 294 " - pdb=" SG  CYS R 296 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.73
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1904

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      40.0% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.974A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.705A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.835A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 4.322A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 3.795A  pdb=" N   ASP A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 306 through 312'
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 3.658A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.495A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.629A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.594A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.949A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.585A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.795A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 54
      removed outlier: 3.848A  pdb=" N   VAL R  36 " --> pdb=" O   ALA R  32 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU R  39 " --> pdb=" O   VAL R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 61
      No H-bonds generated for 'chain 'R' and resid 59 through 61'
    Processing helix  chain 'R' and resid 62 through 77
      removed outlier: 3.814A  pdb=" N   VAL R  66 " --> pdb=" O   ASN R  62 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   SER R  67 " --> pdb=" O   PHE R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 89
      removed outlier: 3.576A  pdb=" N   ALA R  83 " --> pdb=" O   VAL R  79 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 129
      removed outlier: 4.489A  pdb=" N   LEU R 101 " --> pdb=" O   GLY R  97 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU R 117 " --> pdb=" O   SER R 113 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   CYS R 118 " --> pdb=" O   ILE R 114 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LEU R 119 " --> pdb=" O   LEU R 115 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU R 126 " --> pdb=" O   LEU R 122 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 165
      Proline residue:  R 161  - end of helix
    Processing helix  chain 'R' and resid 185 through 224
      removed outlier: 4.133A  pdb=" N   SER R 193 " --> pdb=" O   VAL R 189 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLY R 194 " --> pdb=" O   LEU R 190 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
      removed outlier: 3.501A  pdb=" N   SER R 224 " --> pdb=" O   VAL R 220 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 294
      removed outlier: 3.788A  pdb=" N   PHE R 277 " --> pdb=" O   LEU R 273 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
      removed outlier: 4.233A  pdb=" N   ILE R 289 " --> pdb=" O   PHE R 285 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL R 290 " --> pdb=" O   VAL R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 320
      removed outlier: 3.707A  pdb=" N   VAL R 304 " --> pdb=" O   GLY R 300 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU R 308 " --> pdb=" O   VAL R 304 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   SER R 313 " --> pdb=" O   GLY R 309 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR R 314 " --> pdb=" O   TYR R 310 " (cutoff:3.500A)
      Proline residue:  R 317  - end of helix
    Processing helix  chain 'R' and resid 321 through 323
      No H-bonds generated for 'chain 'R' and resid 321 through 323'
    Processing helix  chain 'R' and resid 324 through 332
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 4.669A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62
      removed outlier: 4.016A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.236A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.710A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.104A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 7.076A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.685A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320
      removed outlier: 3.850A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.369A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL N 124 " --> pdb=" O   ALA N  92 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA N  92 " --> pdb=" O   VAL N 124 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1065 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2524
        1.34 -     1.46: 1884
        1.46 -     1.59: 3398
        1.59 -     1.71: 0
        1.71 -     1.83: 78
  Bond restraints: 7884
  Sorted by residual:
  bond pdb=" C7  UQL R 501 "
       pdb=" N1  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.384  1.258  0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C7  UQL R 501 "
       pdb=" C8  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.377  1.272  0.105 2.00e-02 2.50e+03 2.75e+01
  bond pdb=" C4  UQL R 501 "
       pdb=" C8  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.437  1.382  0.055 2.00e-02 2.50e+03 7.58e+00
  bond pdb=" C3  UQL R 501 "
       pdb=" C4  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.421  1.462 -0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" C7  UQL R 501 "
       pdb=" C9  UQL R 501 "
    ideal  model  delta    sigma   weight residual
    1.488  1.524 -0.036 2.00e-02 2.50e+03 3.24e+00
  ... (remaining 7879 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 10602
        2.57 -     5.13: 100
        5.13 -     7.70: 8
        7.70 -    10.26: 6
       10.26 -    12.83: 1
  Bond angle restraints: 10717
  Sorted by residual:
  angle pdb=" C   ILE R 319 "
        pdb=" N   TYR R 320 "
        pdb=" CA  TYR R 320 "
      ideal   model   delta    sigma   weight residual
     120.09  114.63    5.46 1.25e+00 6.40e-01 1.91e+01
  angle pdb=" C4  UQL R 501 "
        pdb=" C8  UQL R 501 "
        pdb=" C7  UQL R 501 "
      ideal   model   delta    sigma   weight residual
     106.60  119.43  -12.83 3.00e+00 1.11e-01 1.83e+01
  angle pdb=" N   ASP A 284 "
        pdb=" CA  ASP A 284 "
        pdb=" C   ASP A 284 "
      ideal   model   delta    sigma   weight residual
     114.56  110.35    4.21 1.27e+00 6.20e-01 1.10e+01
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     108.86  113.29   -4.43 1.41e+00 5.03e-01 9.89e+00
  angle pdb=" C5  UQL R 501 "
        pdb=" C4  UQL R 501 "
        pdb=" C8  UQL R 501 "
      ideal   model   delta    sigma   weight residual
     133.36  142.64   -9.28 3.00e+00 1.11e-01 9.58e+00
  ... (remaining 10712 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 4225
       16.36 -    32.72: 345
       32.72 -    49.08: 91
       49.08 -    65.44: 12
       65.44 -    81.80: 11
  Dihedral angle restraints: 4684
    sinusoidal: 1746
      harmonic: 2938
  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  -19.05  -66.95     1      1.00e+01 1.00e-02 5.84e+01
  dihedral pdb=" CB  CYS R 294 "
           pdb=" SG  CYS R 294 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.57   54.57     1      1.00e+01 1.00e-02 4.04e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 868
       0.042 -    0.084: 292
       0.084 -    0.126: 76
       0.126 -    0.167: 8
       0.167 -    0.209: 1
  Chirality restraints: 1245
  Sorted by residual:
  chirality pdb=" CA  TYR R 320 "
            pdb=" N   TYR R 320 "
            pdb=" C   TYR R 320 "
            pdb=" CB  TYR R 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  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    2.58   -0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  ARG A 317 "
            pdb=" N   ARG A 317 "
            pdb=" C   ARG A 317 "
            pdb=" CB  ARG A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 1242 not shown)

  Planarity restraints: 1363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 316 "    0.065 5.00e-02 4.00e+02   9.80e-02 1.54e+01
        pdb=" N   PRO R 317 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO R 317 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO R 317 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  81 "   -0.047 5.00e-02 4.00e+02   7.06e-02 7.98e+00
        pdb=" N   PRO R  82 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO R  82 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO R  82 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.041 5.00e-02 4.00e+02   6.21e-02 6.16e+00
        pdb=" N   PRO G  49 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1360 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 248
        2.72 -     3.26: 7458
        3.26 -     3.81: 11670
        3.81 -     4.35: 13997
        4.35 -     4.90: 24766
  Nonbonded interactions: 58139
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   PRO A 361 "
            pdb=" ND1 HIS A 362 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   TYR A 318 "
            pdb=" NH1 ARG A 336 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   MET R 276 "
            pdb=" OG1 THR R 280 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" NH1 ARG N  67 "
            pdb=" O   SER N  85 "
     model   vdw
     2.300 3.120
  ... (remaining 58134 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.430
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.340
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
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      :  0.005   0.126   7884  Z= 0.313
  Angle     :  0.710  12.829  10717  Z= 0.391
  Chirality :  0.044   0.209   1245
  Planarity :  0.006   0.098   1363
  Dihedral  : 13.325  81.800   2768
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.25 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.27), residues: 997
  helix:  0.64 (0.28), residues: 370
  sheet: -0.20 (0.35), residues: 219
  loop : -1.36 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.004   0.002   HIS A  41 
 PHE   0.019   0.002   PHE B 278 
 TYR   0.021   0.002   TYR R 320 
 ARG   0.007   0.001   ARG A 317 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A  392 GLU cc_start: 0.7239 (mm-30) cc_final: 0.7023 (mm-30)
REVERT: R   35 VAL cc_start: 0.8814 (p) cc_final: 0.8591 (m)
REVERT: R   74 MET cc_start: 0.6426 (tmm) cc_final: 0.6130 (tmm)
REVERT: R  127 LEU cc_start: 0.8572 (tp) cc_final: 0.8273 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2639
  time to fit residues: 54.4243
Evaluate side-chains
  152 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 218 ASN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.139699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119038 restraints weight = 11229.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.10
r_work: 0.3410 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.0873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7884  Z= 0.221
  Angle     :  0.556   5.704  10717  Z= 0.298
  Chirality :  0.042   0.173   1245
  Planarity :  0.005   0.069   1363
  Dihedral  :  4.562  17.182   1092
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.14 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.27), residues: 997
  helix:  1.31 (0.28), residues: 374
  sheet: -0.15 (0.34), residues: 235
  loop : -1.29 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.006   0.002   HIS A 220 
 PHE   0.016   0.002   PHE B 278 
 TYR   0.020   0.002   TYR R 320 
 ARG   0.003   0.000   ARG N  67 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 160
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7812 (mt-10)
REVERT: A  392 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8001 (mm-30)
REVERT: R   35 VAL cc_start: 0.8688 (p) cc_final: 0.8434 (m)
REVERT: R   74 MET cc_start: 0.6850 (tmm) cc_final: 0.6333 (tmm)
REVERT: R  276 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7135 (tpp)
  outliers start: 7
  outliers final: 2
  residues processed: 162
  average time/residue: 0.2565
  time to fit residues: 52.8113
Evaluate side-chains
  159 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain R residue  276 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0970
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
N  31 ASN
R  86 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.139915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119266 restraints weight = 11296.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.09
r_work: 0.3416 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7884  Z= 0.203
  Angle     :  0.521   5.520  10717  Z= 0.277
  Chirality :  0.041   0.157   1245
  Planarity :  0.005   0.067   1363
  Dihedral  :  4.330  15.662   1092
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.59 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.27), residues: 997
  helix:  1.58 (0.28), residues: 376
  sheet:  0.04 (0.34), residues: 235
  loop : -1.30 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.014   0.001   PHE B 278 
 TYR   0.015   0.001   TYR A  37 
 ARG   0.002   0.000   ARG B 251 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.868 
Fit side-chains
REVERT: A  392 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7969 (mm-30)
REVERT: B  331 SER cc_start: 0.8425 (t) cc_final: 0.8145 (p)
REVERT: R   35 VAL cc_start: 0.8606 (p) cc_final: 0.8375 (m)
REVERT: R   74 MET cc_start: 0.6830 (tmm) cc_final: 0.6296 (tmm)
REVERT: R  210 ARG cc_start: 0.7901 (mmt90) cc_final: 0.7472 (mmt90)
  outliers start: 15
  outliers final: 10
  residues processed: 165
  average time/residue: 0.2506
  time to fit residues: 53.0636
Evaluate side-chains
  165 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  156 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 77 optimal weight:   20.0000
   chunk 22 optimal weight:    0.3980
   chunk 66 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 279 ASN
R 316 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.136572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.116132 restraints weight = 11313.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.09
r_work: 0.3363 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7884  Z= 0.350
  Angle     :  0.590   5.533  10717  Z= 0.316
  Chirality :  0.044   0.161   1245
  Planarity :  0.005   0.063   1363
  Dihedral  :  4.643  17.879   1092
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.44 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.27), residues: 997
  helix:  1.50 (0.28), residues: 375
  sheet: -0.05 (0.35), residues: 225
  loop : -1.28 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.006   0.002   HIS A 220 
 PHE   0.022   0.002   PHE B 234 
 TYR   0.019   0.002   TYR A  37 
 ARG   0.004   0.000   ARG B 251 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  284 ASP cc_start: 0.7593 (t0) cc_final: 0.7221 (t0)
REVERT: A  392 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8055 (mm-30)
REVERT: R   74 MET cc_start: 0.6786 (tmm) cc_final: 0.6086 (tmm)
  outliers start: 22
  outliers final: 17
  residues processed: 172
  average time/residue: 0.2628
  time to fit residues: 57.2582
Evaluate side-chains
  176 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   77 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  123 ASP
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.119272 restraints weight = 11167.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.10
r_work: 0.3404 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7884  Z= 0.172
  Angle     :  0.503   8.263  10717  Z= 0.266
  Chirality :  0.040   0.144   1245
  Planarity :  0.004   0.064   1363
  Dihedral  :  4.204  15.596   1092
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.93 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.27), residues: 997
  helix:  1.81 (0.28), residues: 377
  sheet:  0.14 (0.35), residues: 226
  loop : -1.23 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.015   0.001   TYR A  37 
 ARG   0.003   0.000   ARG B 251 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 ASP cc_start: 0.7523 (t0) cc_final: 0.7148 (t0)
REVERT: A  392 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: A  393 LEU cc_start: 0.7929 (mt) cc_final: 0.7549 (mp)
REVERT: B   61 MET cc_start: 0.8130 (ppp) cc_final: 0.7165 (ppp)
REVERT: B  220 GLN cc_start: 0.7780 (mt0) cc_final: 0.7519 (mt0)
REVERT: R   74 MET cc_start: 0.6649 (tmm) cc_final: 0.6085 (tmm)
REVERT: R  210 ARG cc_start: 0.7930 (mmt90) cc_final: 0.7492 (mmt90)
  outliers start: 19
  outliers final: 16
  residues processed: 165
  average time/residue: 0.2622
  time to fit residues: 54.7898
Evaluate side-chains
  165 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0970
   chunk 59 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0870
   overall best weight:    0.5360

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.140496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.120117 restraints weight = 11263.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.09
r_work: 0.3422 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7884  Z= 0.153
  Angle     :  0.487   7.504  10717  Z= 0.254
  Chirality :  0.039   0.145   1245
  Planarity :  0.004   0.063   1363
  Dihedral  :  3.997  14.978   1092
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.79 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.28), residues: 997
  helix:  2.04 (0.28), residues: 378
  sheet:  0.23 (0.34), residues: 238
  loop : -1.08 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.014   0.001   TYR A  37 
 ARG   0.004   0.000   ARG B 251 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A  216 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7759 (mmpt)
REVERT: A  284 ASP cc_start: 0.7450 (t0) cc_final: 0.7075 (t0)
REVERT: A  393 LEU cc_start: 0.7867 (mt) cc_final: 0.7492 (mp)
REVERT: B   61 MET cc_start: 0.8144 (ppp) cc_final: 0.7051 (ppp)
REVERT: B  220 GLN cc_start: 0.7804 (mt0) cc_final: 0.7543 (mt0)
REVERT: R   74 MET cc_start: 0.6608 (tmm) cc_final: 0.6078 (tmm)
REVERT: R  210 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7464 (mmt90)
  outliers start: 19
  outliers final: 13
  residues processed: 162
  average time/residue: 0.2493
  time to fit residues: 51.7994
Evaluate side-chains
  160 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  220 VAL
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0060
   chunk 40 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 89 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.5196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.119730 restraints weight = 11212.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.07
r_work: 0.3440 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7884  Z= 0.147
  Angle     :  0.486   7.082  10717  Z= 0.252
  Chirality :  0.039   0.168   1245
  Planarity :  0.004   0.062   1363
  Dihedral  :  3.936  15.702   1092
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.78 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.28), residues: 997
  helix:  2.17 (0.28), residues: 377
  sheet:  0.27 (0.34), residues: 238
  loop : -1.00 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 234 
 TYR   0.014   0.001   TYR A  37 
 ARG   0.004   0.000   ARG A  38 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  213 GLN cc_start: 0.7818 (pt0) cc_final: 0.7485 (pp30)
REVERT: A  284 ASP cc_start: 0.7430 (t0) cc_final: 0.7063 (t0)
REVERT: A  393 LEU cc_start: 0.7814 (mt) cc_final: 0.7455 (mp)
REVERT: B   52 ARG cc_start: 0.8224 (mtt90) cc_final: 0.8009 (mtt90)
REVERT: B   61 MET cc_start: 0.8155 (ppp) cc_final: 0.7081 (ppp)
REVERT: B  220 GLN cc_start: 0.7805 (mt0) cc_final: 0.7554 (mt0)
REVERT: R   74 MET cc_start: 0.6677 (tmm) cc_final: 0.6104 (tmm)
REVERT: R  210 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7453 (mmt90)
  outliers start: 18
  outliers final: 16
  residues processed: 163
  average time/residue: 0.2403
  time to fit residues: 50.1184
Evaluate side-chains
  166 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   77 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  220 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 390 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.136300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.115874 restraints weight = 11294.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.10
r_work: 0.3366 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7884  Z= 0.359
  Angle     :  0.608   6.900  10717  Z= 0.319
  Chirality :  0.044   0.169   1245
  Planarity :  0.005   0.059   1363
  Dihedral  :  4.528  17.697   1092
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.78 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.27), residues: 997
  helix:  1.83 (0.28), residues: 378
  sheet:  0.16 (0.35), residues: 225
  loop : -1.13 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.008   0.002   HIS A 220 
 PHE   0.022   0.002   PHE B 234 
 TYR   0.017   0.002   TYR N  95 
 ARG   0.005   0.000   ARG B 251 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 ASP cc_start: 0.7647 (t0) cc_final: 0.7227 (t0)
REVERT: A  392 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8021 (mm-30)
REVERT: B  220 GLN cc_start: 0.8013 (mt0) cc_final: 0.7763 (mt0)
REVERT: B  259 GLN cc_start: 0.8434 (mt0) cc_final: 0.8142 (mt0)
REVERT: R  210 ARG cc_start: 0.7940 (mmt90) cc_final: 0.7513 (mmt90)
  outliers start: 20
  outliers final: 17
  residues processed: 168
  average time/residue: 0.2545
  time to fit residues: 54.0769
Evaluate side-chains
  173 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   61 SER
Chi-restraints excluded: chain R residue   74 MET
Chi-restraints excluded: chain R residue   77 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 78 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 62 optimal weight:    0.4980
   chunk 40 optimal weight:    0.1980
   chunk 94 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0170
   chunk 50 optimal weight:    0.9990
   chunk 93 optimal weight:    0.3980
   chunk 81 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 279 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.141527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.120806 restraints weight = 11370.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.14
r_work: 0.3431 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7884  Z= 0.140
  Angle     :  0.494   6.562  10717  Z= 0.256
  Chirality :  0.040   0.158   1245
  Planarity :  0.004   0.062   1363
  Dihedral  :  3.995  14.557   1092
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.64 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.27), residues: 997
  helix:  2.10 (0.28), residues: 380
  sheet:  0.25 (0.35), residues: 223
  loop : -1.01 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.013   0.001   TYR A  37 
 ARG   0.004   0.000   ARG A  38 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7806 (mmmm)
REVERT: A  284 ASP cc_start: 0.7516 (t0) cc_final: 0.7093 (t0)
REVERT: A  317 ARG cc_start: 0.7612 (ptm160) cc_final: 0.7359 (ptm160)
REVERT: A  390 GLN cc_start: 0.7467 (tt0) cc_final: 0.7125 (tt0)
REVERT: A  393 LEU cc_start: 0.7848 (mt) cc_final: 0.7464 (mp)
REVERT: B   61 MET cc_start: 0.8106 (ppp) cc_final: 0.7201 (ppp)
REVERT: B  119 ASN cc_start: 0.7638 (m-40) cc_final: 0.7345 (m110)
REVERT: B  220 GLN cc_start: 0.7853 (mt0) cc_final: 0.7637 (mt0)
REVERT: B  259 GLN cc_start: 0.8362 (mt0) cc_final: 0.8126 (mt0)
REVERT: N   39 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8109 (tt0)
REVERT: R  210 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7473 (mmt90)
  outliers start: 14
  outliers final: 12
  residues processed: 161
  average time/residue: 0.2611
  time to fit residues: 53.6949
Evaluate side-chains
  164 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   77 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0010
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    0.0010
   chunk 10 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   chunk 78 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.142049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.121284 restraints weight = 11240.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.11
r_work: 0.3438 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7884  Z= 0.146
  Angle     :  0.497   7.535  10717  Z= 0.255
  Chirality :  0.039   0.154   1245
  Planarity :  0.004   0.061   1363
  Dihedral  :  3.908  16.694   1092
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.64 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.28), residues: 997
  helix:  2.21 (0.28), residues: 380
  sheet:  0.29 (0.35), residues: 229
  loop : -0.88 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.010   0.001   PHE A 222 
 TYR   0.014   0.001   TYR A  37 
 ARG   0.004   0.000   ARG A  38 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 ASP cc_start: 0.7531 (t0) cc_final: 0.7095 (t0)
REVERT: A  317 ARG cc_start: 0.7597 (ptm160) cc_final: 0.7345 (ptm160)
REVERT: A  390 GLN cc_start: 0.7414 (tt0) cc_final: 0.7075 (tt0)
REVERT: A  393 LEU cc_start: 0.7782 (mt) cc_final: 0.7405 (mp)
REVERT: B   61 MET cc_start: 0.8133 (ppp) cc_final: 0.7063 (ppp)
REVERT: B  220 GLN cc_start: 0.7843 (mt0) cc_final: 0.7642 (mt0)
REVERT: N   39 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8111 (tt0)
REVERT: R  210 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7442 (mmt90)
  outliers start: 14
  outliers final: 13
  residues processed: 164
  average time/residue: 0.2550
  time to fit residues: 53.1512
Evaluate side-chains
  165 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   77 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 92 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.140503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.119882 restraints weight = 11246.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.08
r_work: 0.3433 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7884  Z= 0.170
  Angle     :  0.512   9.303  10717  Z= 0.262
  Chirality :  0.040   0.152   1245
  Planarity :  0.004   0.061   1363
  Dihedral  :  3.947  16.796   1092
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.01 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.28), residues: 997
  helix:  2.24 (0.28), residues: 380
  sheet:  0.28 (0.34), residues: 229
  loop : -0.88 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.015   0.001   TYR A  37 
 ARG   0.004   0.000   ARG A  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4830.77 seconds
wall clock time: 83 minutes 8.49 seconds (4988.49 seconds total)