Starting phenix.real_space_refine
on Wed Mar 12 15:44:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h4k_34479/03_2025/8h4k_34479_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h4k_34479/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h4k_34479/03_2025/8h4k_34479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h4k_34479/03_2025/8h4k_34479.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h4k_34479/03_2025/8h4k_34479_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h4k_34479/03_2025/8h4k_34479_neut.cif"
  }
  resolution = 3.1
  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=   0.035 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 6, 'ASP: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, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7}
          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: 5.27, per 1000 atoms: 0.65
  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: 2.38
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.90
  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: 2.38

  Time building geometry restraints manager: 2.59 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:             4.760
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.760
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.060
-------------------------------------------------------------------------------
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   8245  Z= 0.378
  Angle     :  0.733   9.361  11226  Z= 0.413
  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 : 4.14
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 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
 TRP   0.022   0.003   TRP B  82 
 HIS   0.018   0.002   HIS A 357 
 PHE   0.024   0.003   PHE B 151 
 TYR   0.020   0.002   TYR R 247 
 ARG   0.009   0.001   ARG N  72 

*********************** 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  : 1.186 
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: 0.2523
  time to fit residues: 34.0250
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  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0050
   chunk 92 optimal weight:    0.0020
   overall best weight:    0.5002

-------------------------------------------------------------------------------
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 = 0.122242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.094550 restraints weight = 12778.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.12
r_work: 0.3148 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8245  Z= 0.161
  Angle     :  0.539   7.215  11226  Z= 0.290
  Chirality :  0.042   0.150   1317
  Planarity :  0.004   0.057   1424
  Dihedral  :  5.493  54.759   1145
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  5.18 %
    Favored  : 94.12 %
  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:  0.64 (0.26), residues: 1041
  helix:  1.84 (0.27), residues: 398
  sheet:  0.69 (0.33), residues: 241
  loop : -1.23 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.011   0.001   TYR N  80 
 ARG   0.004   0.000   ARG R  68 

*********************** 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  : 0.880 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7444 (t)
REVERT: R   37 LEU cc_start: 0.6506 (pt) cc_final: 0.6298 (mt)
REVERT: R   89 ILE cc_start: 0.8496 (tp) cc_final: 0.8203 (tp)
REVERT: R  213 THR cc_start: 0.7723 (t) cc_final: 0.7496 (t)
  outliers start: 6
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1680
  time to fit residues: 22.8208
Evaluate side-chains
  85 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
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 33 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0170
   chunk 68 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.1022

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.121727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.093311 restraints weight = 13116.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.24
r_work: 0.3098 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8245  Z= 0.239
  Angle     :  0.572   7.967  11226  Z= 0.305
  Chirality :  0.043   0.148   1317
  Planarity :  0.004   0.051   1424
  Dihedral  :  5.340  53.947   1145
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  8.35 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: 1041
  helix:  1.91 (0.27), residues: 398
  sheet:  0.61 (0.34), residues: 236
  loop : -1.06 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.010   0.002   HIS A 357 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.013   0.002   TYR N  95 
 ARG   0.004   0.000   ARG A 232 

*********************** 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
  94 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.334 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7379 (t)
REVERT: B  135 VAL cc_start: 0.8828 (t) cc_final: 0.8507 (p)
REVERT: R   37 LEU cc_start: 0.6553 (pt) cc_final: 0.6303 (mt)
REVERT: R   89 ILE cc_start: 0.8602 (tp) cc_final: 0.8282 (tp)
REVERT: R  213 THR cc_start: 0.7633 (t) cc_final: 0.7403 (t)
  outliers start: 12
  outliers final: 7
  residues processed: 89
  average time/residue: 0.1874
  time to fit residues: 24.5040
Evaluate side-chains
  87 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    7.9990
   chunk 63 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0170
   chunk 80 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.6418

-------------------------------------------------------------------------------
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 = 0.121902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.093782 restraints weight = 13034.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.18
r_work: 0.3137 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8245  Z= 0.164
  Angle     :  0.513   5.867  11226  Z= 0.276
  Chirality :  0.042   0.145   1317
  Planarity :  0.004   0.047   1424
  Dihedral  :  5.010  54.134   1145
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.12 %
    Favored  : 88.47 %
  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:  0.89 (0.27), residues: 1041
  helix:  2.17 (0.28), residues: 392
  sheet:  0.67 (0.33), residues: 244
  loop : -1.07 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.003   0.000   ARG A 232 

*********************** 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
  90 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.937 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7356 (t)
REVERT: B  135 VAL cc_start: 0.8793 (t) cc_final: 0.8469 (p)
REVERT: R   89 ILE cc_start: 0.8511 (tp) cc_final: 0.8176 (tp)
REVERT: R  213 THR cc_start: 0.7565 (t) cc_final: 0.7324 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1732
  time to fit residues: 21.5888
Evaluate side-chains
  86 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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 52 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0070
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 63 optimal weight:    0.2980
   chunk 95 optimal weight:    6.9990
   overall best weight:    1.0002

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.120827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.092719 restraints weight = 12920.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.17
r_work: 0.3115 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8245  Z= 0.218
  Angle     :  0.546   7.328  11226  Z= 0.292
  Chirality :  0.043   0.149   1317
  Planarity :  0.004   0.047   1424
  Dihedral  :  5.011  53.270   1145
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.29 %
    Favored  : 87.06 %
  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:  0.89 (0.27), residues: 1041
  helix:  2.16 (0.27), residues: 392
  sheet:  0.63 (0.34), residues: 245
  loop : -1.03 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.017   0.002   PHE B 151 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.003   0.000   ARG A 232 

*********************** 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
  92 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.944 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8804 (t) cc_final: 0.8489 (p)
REVERT: R   89 ILE cc_start: 0.8581 (tp) cc_final: 0.8233 (tp)
REVERT: R  213 THR cc_start: 0.7592 (t) cc_final: 0.7348 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1753
  time to fit residues: 21.8892
Evaluate side-chains
  87 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0370
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.122333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.095280 restraints weight = 12973.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.25
r_work: 0.3133 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8245  Z= 0.156
  Angle     :  0.499   5.526  11226  Z= 0.269
  Chirality :  0.041   0.144   1317
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.790  53.680   1145
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.00 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.27), residues: 1041
  helix:  2.41 (0.27), residues: 387
  sheet:  0.70 (0.33), residues: 248
  loop : -1.03 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.002   0.000   ARG R  68 

*********************** 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
  93 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 1.078 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7384 (t)
REVERT: B  135 VAL cc_start: 0.8784 (t) cc_final: 0.8472 (p)
REVERT: R   89 ILE cc_start: 0.8560 (tp) cc_final: 0.8210 (tp)
REVERT: R  213 THR cc_start: 0.7557 (t) cc_final: 0.7306 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 86
  average time/residue: 0.1960
  time to fit residues: 26.4685
Evaluate side-chains
  88 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.859 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 1 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0050
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0010
   chunk 81 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5000

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.122996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.095135 restraints weight = 12977.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.40
r_work: 0.3163 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8245  Z= 0.143
  Angle     :  0.485   5.465  11226  Z= 0.260
  Chirality :  0.041   0.212   1317
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.625  54.155   1145
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.35 %
    Favored  : 86.00 %
  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:  1.18 (0.27), residues: 1041
  helix:  2.51 (0.27), residues: 388
  sheet:  0.82 (0.33), residues: 246
  loop : -1.00 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R 263 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.002   0.000   ARG R  68 

*********************** 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
  92 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.926 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7348 (t)
REVERT: B  135 VAL cc_start: 0.8778 (t) cc_final: 0.8464 (p)
REVERT: N   31 ASN cc_start: 0.8560 (m-40) cc_final: 0.8355 (m110)
REVERT: R   89 ILE cc_start: 0.8501 (tp) cc_final: 0.8237 (tp)
REVERT: R  213 THR cc_start: 0.7615 (t) cc_final: 0.7352 (t)
  outliers start: 14
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1786
  time to fit residues: 22.4045
Evaluate side-chains
  90 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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   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  196 LEU
Chi-restraints excluded: chain R residue  233 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0020
   chunk 14 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.124841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.096999 restraints weight = 13136.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.37
r_work: 0.3150 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8245  Z= 0.152
  Angle     :  0.488   5.647  11226  Z= 0.262
  Chirality :  0.042   0.209   1317
  Planarity :  0.004   0.045   1424
  Dihedral  :  4.578  53.729   1145
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.27), residues: 1041
  helix:  2.58 (0.27), residues: 388
  sheet:  0.77 (0.33), residues: 248
  loop : -0.92 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.002   0.000   ARG R  68 

*********************** 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
  93 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A   60 MET cc_start: 0.6792 (mtp) cc_final: 0.6572 (mtp)
REVERT: B  135 VAL cc_start: 0.8776 (t) cc_final: 0.8460 (p)
REVERT: N   31 ASN cc_start: 0.8604 (m-40) cc_final: 0.8388 (m110)
REVERT: R   89 ILE cc_start: 0.8507 (tp) cc_final: 0.8170 (tp)
REVERT: R  213 THR cc_start: 0.7568 (t) cc_final: 0.7317 (t)
REVERT: R  296 LEU cc_start: 0.7228 (mt) cc_final: 0.6884 (tt)
  outliers start: 13
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1758
  time to fit residues: 22.5275
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  : 0.946 
-------------------------------------------------------------------------------
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   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  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 79 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0370
   chunk 31 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 3 optimal weight:    0.1980
   chunk 88 optimal weight:    0.7980
   chunk 45 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 85 optimal weight:    0.2980
   overall best weight:    0.2658

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.125882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.097957 restraints weight = 13074.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.42
r_work: 0.3208 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8245  Z= 0.118
  Angle     :  0.452   6.224  11226  Z= 0.242
  Chirality :  0.041   0.216   1317
  Planarity :  0.003   0.045   1424
  Dihedral  :  4.340  54.132   1145
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.27), residues: 1041
  helix:  2.73 (0.27), residues: 388
  sheet:  0.70 (0.33), residues: 248
  loop : -0.84 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R 263 
 TYR   0.006   0.001   TYR N  95 
 ARG   0.002   0.000   ARG R  68 

*********************** 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
  101 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.906 
Fit side-chains
REVERT: B  133 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7339 (t)
REVERT: B  135 VAL cc_start: 0.8756 (t) cc_final: 0.8441 (p)
REVERT: N   20 LEU cc_start: 0.7380 (mt) cc_final: 0.7016 (mp)
REVERT: R   65 VAL cc_start: 0.5528 (t) cc_final: 0.5302 (p)
REVERT: R  213 THR cc_start: 0.7573 (t) cc_final: 0.7321 (t)
REVERT: R  296 LEU cc_start: 0.7039 (mt) cc_final: 0.6778 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 96
  average time/residue: 0.1688
  time to fit residues: 23.7773
Evaluate side-chains
  98 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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 R residue  135 GLU
Chi-restraints excluded: chain R residue  196 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 60 optimal weight:    0.1980
   chunk 97 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R 112 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.123353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.095356 restraints weight = 13012.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.53
r_work: 0.3152 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8245  Z= 0.161
  Angle     :  0.503   7.737  11226  Z= 0.267
  Chirality :  0.042   0.226   1317
  Planarity :  0.004   0.045   1424
  Dihedral  :  4.416  51.966   1145
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.27), residues: 1041
  helix:  2.71 (0.27), residues: 388
  sheet:  0.77 (0.33), residues: 250
  loop : -0.80 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.002   0.000   ARG A 232 

********************** 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
  96 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.942 
Fit side-chains
REVERT: B  135 VAL cc_start: 0.8807 (t) cc_final: 0.8494 (p)
REVERT: N   20 LEU cc_start: 0.7524 (mt) cc_final: 0.7128 (mp)
REVERT: R  213 THR cc_start: 0.7652 (t) cc_final: 0.7398 (t)
REVERT: R  296 LEU cc_start: 0.7067 (mt) cc_final: 0.6795 (tt)
  outliers start: 11
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1741
  time to fit residues: 23.1253
Evaluate side-chains
  94 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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  196 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 112 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.122279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.094345 restraints weight = 12996.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.33
r_work: 0.3145 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8245  Z= 0.188
  Angle     :  0.525   7.305  11226  Z= 0.280
  Chirality :  0.043   0.222   1317
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.475  49.391   1145
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.88 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.27), residues: 1041
  helix:  2.70 (0.27), residues: 388
  sheet:  0.75 (0.33), residues: 250
  loop : -0.82 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.017   0.002   HIS R 112 
 PHE   0.019   0.002   PHE R 263 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.002   0.000   ARG A 232 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4760.75 seconds
wall clock time: 83 minutes 2.13 seconds (4982.13 seconds total)