Starting phenix.real_space_refine
on Fri Aug 22 21:26:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h4k_34479/08_2025/8h4k_34479_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h4k_34479/08_2025/8h4k_34479.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h4k_34479/08_2025/8h4k_34479_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h4k_34479/08_2025/8h4k_34479_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h4k_34479/08_2025/8h4k_34479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h4k_34479/08_2025/8h4k_34479.map"
  }
  resolution = 3.1
  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=   0.035 sd=   0.128
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      48      5.16       5
     C    5158      2.51       5
     N    1380      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8078
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1857
          Classifications: {'peptide': 234}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2533
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "G"
      Number of atoms: 402
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 402
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2290
          Classifications: {'peptide': 299}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 13, 'TRANS': 285}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 2, 'GLN:plan1': 4}
          Unresolved non-hydrogen planarities: 59
    Chain: "R"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'WPT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.28
  Number of scatterers: 8078
  At special positions: 0
  Unit cell: (80.3, 102.3, 137.5, 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      48     16.00
     O    1492      8.00
     N    1380      7.00
     C    5158      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 477.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      41.0% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 38
      removed outlier: 3.999A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.777A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.518A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 235 through 239'
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.587A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ASN A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 4.220A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.918A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.545A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.725A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.755A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.569A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.506A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.941A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.600A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 35 through 67
      removed outlier: 3.566A  pdb=" N   ARG R  67 " --> pdb=" O   VAL R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 89
      removed outlier: 3.997A  pdb=" N   ASN R  80 " --> pdb=" O   CYS R  76 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 102
      removed outlier: 3.653A  pdb=" N   VAL R  95 " --> pdb=" O   ALA R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 107 through 143
      removed outlier: 5.481A  pdb=" N   PHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL R 141 " --> pdb=" O   MET R 137 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU R 143 " --> pdb=" O   CYS R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 169
    Processing helix  chain 'R' and resid 171 through 176
    Processing helix  chain 'R' and resid 200 through 216
    Processing helix  chain 'R' and resid 216 through 244
      removed outlier: 3.633A  pdb=" N   GLY R 220 " --> pdb=" O   PHE R 216 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS R 239 " --> pdb=" O   LYS R 235 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ARG R 240 " --> pdb=" O   ALA R 236 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   LEU R 241 " --> pdb=" O   SER R 237 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   THR R 242 " --> pdb=" O   ARG R 238 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 251 through 256
      removed outlier: 3.861A  pdb=" N   SER R 256 " --> pdb=" O   GLN R 252 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 276
      removed outlier: 4.168A  pdb=" N   PHE R 273 " --> pdb=" O   LEU R 269 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE R 274 " --> pdb=" O   MET R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 293
    Processing helix  chain 'R' and resid 299 through 311
      removed outlier: 3.624A  pdb=" N   PHE R 303 " --> pdb=" O   TRP R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 321
      Proline residue:  R 318  - end of helix
      removed outlier: 3.514A  pdb=" N   TYR R 321 " --> pdb=" O   ASN R 317 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.991A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.961A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.994A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.061A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.948A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.916A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.756A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.697A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.939A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 177 through 182

    400 hydrogen bonds defined for protein.
    1149 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: 1.25

  Time building geometry restraints manager: 0.84 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: 2621
        1.34 -     1.46: 1924
        1.46 -     1.58: 3634
        1.58 -     1.71: 0
        1.71 -     1.83: 66
  Bond restraints: 8245
  Sorted by residual:
  bond pdb=" C16 WPT R 401 "
       pdb=" N15 WPT R 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.455 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" C12 WPT R 401 "
       pdb=" C14 WPT R 401 "
    ideal  model  delta    sigma   weight residual
    1.505  1.564 -0.059 2.00e-02 2.50e+03 8.80e+00
  bond pdb=" C08 WPT R 401 "
       pdb=" O07 WPT R 401 "
    ideal  model  delta    sigma   weight residual
    1.381  1.433 -0.052 2.00e-02 2.50e+03 6.73e+00
  bond pdb=" C04 WPT R 401 "
       pdb=" O07 WPT R 401 "
    ideal  model  delta    sigma   weight residual
    1.381  1.430 -0.049 2.00e-02 2.50e+03 6.10e+00
  bond pdb=" C19 WPT R 401 "
       pdb=" C22 WPT R 401 "
    ideal  model  delta    sigma   weight residual
    1.506  1.543 -0.037 2.00e-02 2.50e+03 3.50e+00
  ... (remaining 8240 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 10913
        1.87 -     3.74: 269
        3.74 -     5.62: 33
        5.62 -     7.49: 10
        7.49 -     9.36: 1
  Bond angle restraints: 11226
  Sorted by residual:
  angle pdb=" N   GLU A  15 "
        pdb=" CA  GLU A  15 "
        pdb=" C   GLU A  15 "
      ideal   model   delta    sigma   weight residual
     114.04  108.73    5.31 1.24e+00 6.50e-01 1.83e+01
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     110.06  114.77   -4.71 1.43e+00 4.89e-01 1.09e+01
  angle pdb=" C   LEU B 261 "
        pdb=" N   MET B 262 "
        pdb=" CA  MET B 262 "
      ideal   model   delta    sigma   weight residual
     121.85  116.49    5.36 1.77e+00 3.19e-01 9.16e+00
  angle pdb=" C   ASP A 252 "
        pdb=" N   TYR A 253 "
        pdb=" CA  TYR A 253 "
      ideal   model   delta    sigma   weight residual
     121.54  127.04   -5.50 1.91e+00 2.74e-01 8.30e+00
  angle pdb=" CA  LEU B  79 "
        pdb=" CB  LEU B  79 "
        pdb=" CG  LEU B  79 "
      ideal   model   delta    sigma   weight residual
     116.30  125.66   -9.36 3.50e+00 8.16e-02 7.15e+00
  ... (remaining 11221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 4439
       17.56 -    35.11: 348
       35.11 -    52.67: 49
       52.67 -    70.22: 19
       70.22 -    87.78: 6
  Dihedral angle restraints: 4861
    sinusoidal: 1794
      harmonic: 3067
  Sorted by residual:
  dihedral pdb=" CA  GLY B 202 "
           pdb=" C   GLY B 202 "
           pdb=" N   ALA B 203 "
           pdb=" CA  ALA B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.82  -25.18     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  LEU B 308 "
           pdb=" C   LEU B 308 "
           pdb=" N   ALA B 309 "
           pdb=" CA  ALA B 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.92  -23.08     0      5.00e+00 4.00e-02 2.13e+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 -157.98  -22.02     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 4858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 718
       0.034 -    0.068: 413
       0.068 -    0.102: 126
       0.102 -    0.136: 54
       0.136 -    0.170: 6
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CA  ILE N  58 "
            pdb=" N   ILE N  58 "
            pdb=" C   ILE N  58 "
            pdb=" CB  ILE N  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  ILE B 120 "
            pdb=" N   ILE B 120 "
            pdb=" C   ILE B 120 "
            pdb=" CB  ILE B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.37e-01
  ... (remaining 1314 not shown)

  Planarity restraints: 1424
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  52 "   -0.051 5.00e-02 4.00e+02   7.78e-02 9.69e+00
        pdb=" N   PRO G  53 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO G  53 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO G  53 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B 236 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 171 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.57e+00
        pdb=" N   PRO R 172 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO R 172 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R 172 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1421 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 60
        2.63 -     3.20: 6833
        3.20 -     3.76: 11166
        3.76 -     4.33: 15440
        4.33 -     4.90: 27068
  Nonbonded interactions: 60567
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.061 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.073 3.040
  nonbonded pdb=" OG  SER R  54 "
            pdb=" OG  SER R 314 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ALA A  48 "
            pdb=" OG  SER A  51 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.234 3.040
  ... (remaining 60562 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.580
  Find NCS groups from input model:        0.040
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   8246  Z= 0.246
  Angle     :  0.734   9.361  11228  Z= 0.414
  Chirality :  0.047   0.170   1317
  Planarity :  0.005   0.078   1424
  Dihedral  : 13.570  87.778   2868
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  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 aren not related in a simple way.
  whole:  0.17 (0.26), residues: 1041
  helix:  1.51 (0.27), residues: 392
  sheet:  0.16 (0.32), residues: 244
  loop : -1.31 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N  72 
 TYR   0.020   0.002   TYR R 247 
 PHE   0.024   0.003   PHE B 151 
 TRP   0.022   0.003   TRP B  82 
 HIS   0.018   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 8245)
  covalent geometry    : angle       0.73319 (11226)
  SS BOND              : bond        0.00440 (    1)
  SS BOND              : angle       2.99369 (    2)
  hydrogen bonds       : bond        0.13118 (  400)
  hydrogen bonds       : angle       5.02342 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8543 (t) cc_final: 0.8291 (p)
REVERT: R   89 ILE cc_start: 0.8430 (tp) cc_final: 0.8172 (tp)
REVERT: R  213 THR cc_start: 0.7620 (t) cc_final: 0.7395 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0849
  time to fit residues: 11.5699
Evaluate side-chains
  85 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0030
   chunk 65 optimal weight:    0.0470
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.2980
   overall best weight:    0.1846

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 292 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.123788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.095970 restraints weight = 12983.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.16
r_work: 0.3179 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8246  Z= 0.109
  Angle     :  0.514   6.933  11228  Z= 0.277
  Chirality :  0.042   0.147   1317
  Planarity :  0.004   0.056   1424
  Dihedral  :  5.428  57.152   1145
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  4.59 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.27), residues: 1041
  helix:  2.03 (0.28), residues: 391
  sheet:  0.73 (0.33), residues: 241
  loop : -1.17 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R  68 
 TYR   0.009   0.001   TYR N  80 
 PHE   0.016   0.001   PHE R 263 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 8245)
  covalent geometry    : angle       0.51336 (11226)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       1.80260 (    2)
  hydrogen bonds       : bond        0.04625 (  400)
  hydrogen bonds       : angle       3.95887 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7418 (t)
REVERT: N   20 LEU cc_start: 0.7953 (mt) cc_final: 0.7710 (mp)
REVERT: R   37 LEU cc_start: 0.6404 (pt) cc_final: 0.6181 (mt)
REVERT: R   89 ILE cc_start: 0.8523 (tp) cc_final: 0.8244 (tp)
REVERT: R  213 THR cc_start: 0.7744 (t) cc_final: 0.7514 (t)
  outliers start: 6
  outliers final: 4
  residues processed: 93
  average time/residue: 0.0724
  time to fit residues: 10.0214
Evaluate side-chains
  88 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  173 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   chunk 100 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.121994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.093756 restraints weight = 12961.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.21
r_work: 0.3098 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8246  Z= 0.158
  Angle     :  0.577   7.624  11228  Z= 0.307
  Chirality :  0.043   0.147   1317
  Planarity :  0.004   0.052   1424
  Dihedral  :  5.300  54.678   1145
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  7.41 %
    Favored  : 90.94 %
  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 aren not related in a simple way.
  whole:  0.76 (0.27), residues: 1041
  helix:  1.95 (0.27), residues: 398
  sheet:  0.62 (0.34), residues: 236
  loop : -1.05 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 232 
 TYR   0.014   0.002   TYR N  95 
 PHE   0.019   0.002   PHE B 151 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.011   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8245)
  covalent geometry    : angle       0.57629 (11226)
  SS BOND              : bond        0.00490 (    1)
  SS BOND              : angle       2.10811 (    2)
  hydrogen bonds       : bond        0.05774 (  400)
  hydrogen bonds       : angle       4.00251 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.311 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8823 (t) cc_final: 0.8503 (p)
REVERT: R   37 LEU cc_start: 0.6504 (pt) cc_final: 0.6241 (mt)
REVERT: R   89 ILE cc_start: 0.8598 (tp) cc_final: 0.8276 (tp)
REVERT: R  213 THR cc_start: 0.7622 (t) cc_final: 0.7385 (t)
  outliers start: 14
  outliers final: 6
  residues processed: 95
  average time/residue: 0.0774
  time to fit residues: 10.3676
Evaluate side-chains
  88 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  173 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.7586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.122980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.094644 restraints weight = 13294.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.57
r_work: 0.3113 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8246  Z= 0.123
  Angle     :  0.526   6.423  11228  Z= 0.282
  Chirality :  0.042   0.147   1317
  Planarity :  0.004   0.047   1424
  Dihedral  :  5.032  53.670   1145
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.65 %
    Favored  : 88.82 %
  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 aren not related in a simple way.
  whole:  0.91 (0.27), residues: 1041
  helix:  2.16 (0.27), residues: 392
  sheet:  0.69 (0.33), residues: 239
  loop : -1.02 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.011   0.001   TYR N  95 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.018   0.002   TRP R 104 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8245)
  covalent geometry    : angle       0.52588 (11226)
  SS BOND              : bond        0.00392 (    1)
  SS BOND              : angle       1.74375 (    2)
  hydrogen bonds       : bond        0.05011 (  400)
  hydrogen bonds       : angle       3.87369 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.185 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7392 (t)
REVERT: B  135 VAL cc_start: 0.8816 (t) cc_final: 0.8497 (p)
REVERT: R   37 LEU cc_start: 0.6516 (pt) cc_final: 0.6215 (mt)
REVERT: R   89 ILE cc_start: 0.8537 (tp) cc_final: 0.8201 (tp)
REVERT: R  213 THR cc_start: 0.7593 (t) cc_final: 0.7351 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 89
  average time/residue: 0.0741
  time to fit residues: 9.5315
Evaluate side-chains
  88 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  173 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 100 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.123911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.096851 restraints weight = 13027.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.33
r_work: 0.3104 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8246  Z= 0.118
  Angle     :  0.514   6.149  11228  Z= 0.275
  Chirality :  0.042   0.152   1317
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.874  53.935   1145
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.06 %
    Favored  : 87.18 %
  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 aren not related in a simple way.
  whole:  0.95 (0.27), residues: 1041
  helix:  2.25 (0.27), residues: 393
  sheet:  0.72 (0.33), residues: 246
  loop : -1.11 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.011   0.001   TYR N  95 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8245)
  covalent geometry    : angle       0.51415 (11226)
  SS BOND              : bond        0.00344 (    1)
  SS BOND              : angle       1.50366 (    2)
  hydrogen bonds       : bond        0.04789 (  400)
  hydrogen bonds       : angle       3.79038 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.285 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7267 (t)
REVERT: B  135 VAL cc_start: 0.8717 (t) cc_final: 0.8413 (p)
REVERT: R   89 ILE cc_start: 0.8523 (tp) cc_final: 0.8234 (tp)
REVERT: R  213 THR cc_start: 0.7537 (t) cc_final: 0.7284 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 90
  average time/residue: 0.0676
  time to fit residues: 8.9228
Evaluate side-chains
  91 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  196 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.120301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.092226 restraints weight = 12863.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.16
r_work: 0.3111 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8246  Z= 0.151
  Angle     :  0.556   7.714  11228  Z= 0.297
  Chirality :  0.043   0.146   1317
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.945  52.766   1145
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.41 %
    Favored  : 86.82 %
  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 aren not related in a simple way.
  whole:  0.97 (0.27), residues: 1041
  helix:  2.32 (0.27), residues: 387
  sheet:  0.58 (0.34), residues: 245
  loop : -1.00 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.013   0.002   TYR N  95 
 PHE   0.019   0.002   PHE B 151 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.010   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8245)
  covalent geometry    : angle       0.55563 (11226)
  SS BOND              : bond        0.00431 (    1)
  SS BOND              : angle       1.77215 (    2)
  hydrogen bonds       : bond        0.05423 (  400)
  hydrogen bonds       : angle       3.88951 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.297 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8795 (t) cc_final: 0.8500 (p)
REVERT: R   89 ILE cc_start: 0.8579 (tp) cc_final: 0.8225 (tp)
REVERT: R  213 THR cc_start: 0.7599 (t) cc_final: 0.7347 (t)
  outliers start: 15
  outliers final: 10
  residues processed: 88
  average time/residue: 0.0693
  time to fit residues: 8.8951
Evaluate side-chains
  88 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   60 CYS
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  173 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0870
   chunk 71 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.122035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.095114 restraints weight = 13109.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.21
r_work: 0.3135 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8246  Z= 0.112
  Angle     :  0.507   5.550  11228  Z= 0.272
  Chirality :  0.042   0.145   1317
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.745  53.116   1145
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.24 %
    Favored  : 86.24 %
  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 aren not related in a simple way.
  whole:  1.07 (0.27), residues: 1041
  helix:  2.45 (0.27), residues: 387
  sheet:  0.70 (0.33), residues: 246
  loop : -1.04 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  68 
 TYR   0.010   0.001   TYR N  95 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8245)
  covalent geometry    : angle       0.50619 (11226)
  SS BOND              : bond        0.00339 (    1)
  SS BOND              : angle       1.50643 (    2)
  hydrogen bonds       : bond        0.04646 (  400)
  hydrogen bonds       : angle       3.76145 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.7414 (t)
REVERT: B  135 VAL cc_start: 0.8787 (t) cc_final: 0.8483 (p)
REVERT: R   89 ILE cc_start: 0.8551 (tp) cc_final: 0.8279 (tp)
REVERT: R  213 THR cc_start: 0.7566 (t) cc_final: 0.7308 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 90
  average time/residue: 0.0737
  time to fit residues: 9.6890
Evaluate side-chains
  92 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  196 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.4986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.119057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.090700 restraints weight = 12947.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.20
r_work: 0.3083 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8246  Z= 0.190
  Angle     :  0.604   8.410  11228  Z= 0.321
  Chirality :  0.044   0.148   1317
  Planarity :  0.004   0.050   1424
  Dihedral  :  5.001  50.902   1145
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.12 %
    Favored  : 85.88 %
  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 aren not related in a simple way.
  whole:  0.94 (0.27), residues: 1041
  helix:  2.27 (0.27), residues: 387
  sheet:  0.53 (0.34), residues: 238
  loop : -0.94 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  42 
 TYR   0.016   0.002   TYR N  95 
 PHE   0.021   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.011   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 8245)
  covalent geometry    : angle       0.60293 (11226)
  SS BOND              : bond        0.00550 (    1)
  SS BOND              : angle       2.09809 (    2)
  hydrogen bonds       : bond        0.06030 (  400)
  hydrogen bonds       : angle       3.98833 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.320 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8791 (t) cc_final: 0.8536 (p)
REVERT: R   89 ILE cc_start: 0.8623 (tp) cc_final: 0.8270 (tp)
REVERT: R  213 THR cc_start: 0.7713 (t) cc_final: 0.7470 (t)
  outliers start: 17
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0657
  time to fit residues: 8.6661
Evaluate side-chains
  88 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   60 CYS
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.121023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.092980 restraints weight = 12919.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.15
r_work: 0.3126 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8246  Z= 0.131
  Angle     :  0.533   6.210  11228  Z= 0.286
  Chirality :  0.042   0.145   1317
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.795  51.242   1145
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.82 %
    Favored  : 85.65 %
  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 aren not related in a simple way.
  whole:  1.02 (0.27), residues: 1041
  helix:  2.40 (0.27), residues: 387
  sheet:  0.61 (0.33), residues: 248
  loop : -1.02 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.012   0.001   TYR N  95 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8245)
  covalent geometry    : angle       0.53273 (11226)
  SS BOND              : bond        0.00401 (    1)
  SS BOND              : angle       1.69379 (    2)
  hydrogen bonds       : bond        0.05092 (  400)
  hydrogen bonds       : angle       3.84042 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.326 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8770 (t) cc_final: 0.8511 (p)
REVERT: R   89 ILE cc_start: 0.8539 (tp) cc_final: 0.8187 (tp)
REVERT: R  213 THR cc_start: 0.7576 (t) cc_final: 0.7318 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 85
  average time/residue: 0.0717
  time to fit residues: 9.0967
Evaluate side-chains
  90 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   60 CYS
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0980
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.121637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.093363 restraints weight = 12979.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.19
r_work: 0.3134 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8246  Z= 0.120
  Angle     :  0.516   6.188  11228  Z= 0.276
  Chirality :  0.042   0.144   1317
  Planarity :  0.004   0.045   1424
  Dihedral  :  4.667  51.460   1145
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.53 %
    Favored  : 85.29 %
  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 aren not related in a simple way.
  whole:  1.14 (0.27), residues: 1041
  helix:  2.53 (0.27), residues: 387
  sheet:  0.66 (0.33), residues: 248
  loop : -0.97 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.010   0.001   TYR N  95 
 PHE   0.020   0.001   PHE R 263 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8245)
  covalent geometry    : angle       0.51584 (11226)
  SS BOND              : bond        0.00362 (    1)
  SS BOND              : angle       1.68195 (    2)
  hydrogen bonds       : bond        0.04739 (  400)
  hydrogen bonds       : angle       3.75765 ( 1149)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.315 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8767 (t) cc_final: 0.8497 (p)
REVERT: R   89 ILE cc_start: 0.8565 (tp) cc_final: 0.8225 (tp)
REVERT: R  213 THR cc_start: 0.7568 (t) cc_final: 0.7309 (t)
  outliers start: 10
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0760
  time to fit residues: 9.1885
Evaluate side-chains
  89 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   60 CYS
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 18 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   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  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.121775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.093489 restraints weight = 12973.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.19
r_work: 0.3134 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8246  Z= 0.122
  Angle     :  0.520   6.245  11228  Z= 0.278
  Chirality :  0.042   0.229   1317
  Planarity :  0.004   0.045   1424
  Dihedral  :  4.635  50.919   1145
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.29 %
    Favored  : 85.18 %
  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 aren not related in a simple way.
  whole:  1.17 (0.27), residues: 1041
  helix:  2.54 (0.27), residues: 387
  sheet:  0.67 (0.33), residues: 248
  loop : -0.95 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.011   0.001   TYR N  95 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8245)
  covalent geometry    : angle       0.51965 (11226)
  SS BOND              : bond        0.00375 (    1)
  SS BOND              : angle       1.62379 (    2)
  hydrogen bonds       : bond        0.04766 (  400)
  hydrogen bonds       : angle       3.75753 ( 1149)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2113.73 seconds
wall clock time: 36 minutes 43.01 seconds (2203.01 seconds total)