Starting phenix.real_space_refine
on Sat Aug 23 00:08:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlk_36400/08_2025/8jlk_36400.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlk_36400/08_2025/8jlk_36400.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlk_36400/08_2025/8jlk_36400.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlk_36400/08_2025/8jlk_36400.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlk_36400/08_2025/8jlk_36400.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlk_36400/08_2025/8jlk_36400.map"
  }
  resolution = 3.22
  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=  -0.002 sd=   0.084
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      63      5.16       5
     C    5617      2.51       5
     N    1506      2.21       5
     O    1638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  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: 8824
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1915
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2084
          Classifications: {'peptide': 268}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 12, 'TRANS': 255}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "S"
      Number of atoms: 1775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1775
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "Y"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "R"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'UJL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.76, per 1000 atoms: 0.20
  Number of scatterers: 8824
  At special positions: 0
  Unit cell: (110.4, 134.32, 105.8, 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      63     16.00
     O    1638      8.00
     N    1506      7.00
     C    5617      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " 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: 0.60
  Conformation dependent library (CDL) restraints added in 452.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 15 sheets defined
      37.6% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.631A  pdb=" N   GLU A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ALA A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.683A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 4.038A  pdb=" N   GLN A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 3.555A  pdb=" N   ASN A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 269
      removed outlier: 3.771A  pdb=" N   LEU A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 298 through 318
      removed outlier: 4.358A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   SER A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA A 318 " --> pdb=" O   ARG A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
      removed outlier: 3.859A  pdb=" N   ARG A 352 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.841A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASP B  20 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 4.195A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 20 through 50
      removed outlier: 3.573A  pdb=" N   VAL R  43 " --> pdb=" O   GLY R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 55 through 85
      removed outlier: 4.462A  pdb=" N   MET R  76 " --> pdb=" O   GLY R  72 " (cutoff:3.500A)
      Proline residue:  R  77  - end of helix
      removed outlier: 3.652A  pdb=" N   THR R  83 " --> pdb=" O   SER R  79 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL R  84 " --> pdb=" O   MET R  80 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLU R  85 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 126
      removed outlier: 3.663A  pdb=" N   CYS R  95 " --> pdb=" O   GLY R  91 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS R  96 " --> pdb=" O   GLU R  92 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL R  97 " --> pdb=" O   ILE R  93 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASP R 126 " --> pdb=" O   CYS R 122 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 134
      removed outlier: 3.695A  pdb=" N   LYS R 133 " --> pdb=" O   ARG R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 135 through 159
      removed outlier: 3.825A  pdb=" N   LEU R 149 " --> pdb=" O   VAL R 145 " (cutoff:3.500A)
      Proline residue:  R 150  - end of helix
    Processing helix  chain 'R' and resid 167 through 174
    Processing helix  chain 'R' and resid 186 through 222
      removed outlier: 4.066A  pdb=" N   VAL R 191 " --> pdb=" O   LYS R 187 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   ILE R 200 " --> pdb=" O   THR R 196 " (cutoff:3.500A)
      Proline residue:  R 201  - end of helix
      removed outlier: 4.118A  pdb=" N   TYR R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE R 214 " --> pdb=" O   TYR R 210 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA R 220 " --> pdb=" O   ALA R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 260
      removed outlier: 4.437A  pdb=" N   PHE R 257 " --> pdb=" O   MET R 253 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 275
      Proline residue:  R 272  - end of helix
    Processing helix  chain 'R' and resid 279 through 303
      removed outlier: 3.662A  pdb=" N   ASN R 283 " --> pdb=" O   PRO R 279 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA R 285 " --> pdb=" O   SER R 281 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY R 290 " --> pdb=" O   LEU R 286 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
      removed outlier: 3.525A  pdb=" N   TYR R 301 " --> pdb=" O   ASN R 297 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 310
      removed outlier: 3.755A  pdb=" N   ARG R 310 " --> pdb=" O   PRO R 306 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.841A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 8 through 24
      removed outlier: 3.690A  pdb=" N   LYS Y  14 " --> pdb=" O   ALA Y  10 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU Y  15 " --> pdb=" O   GLN Y  11 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL Y  16 " --> pdb=" O   ALA Y  12 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN Y  24 " --> pdb=" O   LYS Y  20 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 28 through 45
      removed outlier: 3.910A  pdb=" N   LYS Y  32 " --> pdb=" O   ILE Y  28 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA Y  33 " --> pdb=" O   LYS Y  29 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU Y  37 " --> pdb=" O   ALA Y  33 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190
      removed outlier: 4.787A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 9.900A  pdb=" N   ALA A 220 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.030A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47
      removed outlier: 3.891A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47
      removed outlier: 3.891A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.136A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.053A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.958A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.600A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.515A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.017A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.553A  pdb=" N   SER S   7 " --> pdb=" O   SER S  21 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
    Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.573A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TYR S  94 " --> pdb=" O   THR S 115 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
    Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.529A  pdb=" N   ASN S 194 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1083 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: 1.07

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1434
        1.32 -     1.44: 2537
        1.44 -     1.57: 4956
        1.57 -     1.69: 0
        1.69 -     1.82: 93
  Bond restraints: 9020
  Sorted by residual:
  bond pdb=" CA  PHE R 264 "
       pdb=" C   PHE R 264 "
    ideal  model  delta    sigma   weight residual
    1.524  1.455  0.070 1.24e-02 6.50e+03 3.16e+01
  bond pdb=" C   GLY R 218 "
       pdb=" O   GLY R 218 "
    ideal  model  delta    sigma   weight residual
    1.234  1.287 -0.053 1.20e-02 6.94e+03 1.98e+01
  bond pdb=" N   ARG R 211 "
       pdb=" CA  ARG R 211 "
    ideal  model  delta    sigma   weight residual
    1.459  1.510 -0.051 1.21e-02 6.83e+03 1.74e+01
  bond pdb=" C   PHE R 264 "
       pdb=" N   PHE R 265 "
    ideal  model  delta    sigma   weight residual
    1.335  1.283  0.052 1.34e-02 5.57e+03 1.51e+01
  bond pdb=" C   ILE R 118 "
       pdb=" O   ILE R 118 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.13e-02 7.83e+03 1.45e+01
  ... (remaining 9015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 11827
        2.09 -     4.17: 326
        4.17 -     6.26: 63
        6.26 -     8.35: 10
        8.35 -    10.43: 2
  Bond angle restraints: 12228
  Sorted by residual:
  angle pdb=" N   ARG R  82 "
        pdb=" CA  ARG R  82 "
        pdb=" C   ARG R  82 "
      ideal   model   delta    sigma   weight residual
     113.19  123.62  -10.43 1.19e+00 7.06e-01 7.69e+01
  angle pdb=" O   SER R 117 "
        pdb=" C   SER R 117 "
        pdb=" N   ILE R 118 "
      ideal   model   delta    sigma   weight residual
     122.07  115.61    6.46 1.03e+00 9.43e-01 3.94e+01
  angle pdb=" C   ARG R 211 "
        pdb=" CA  ARG R 211 "
        pdb=" CB  ARG R 211 "
      ideal   model   delta    sigma   weight residual
     110.79  101.72    9.07 1.66e+00 3.63e-01 2.99e+01
  angle pdb=" CA  SER R 117 "
        pdb=" C   SER R 117 "
        pdb=" N   ILE R 118 "
      ideal   model   delta    sigma   weight residual
     117.07  123.27   -6.20 1.14e+00 7.69e-01 2.96e+01
  angle pdb=" C   ILE R 118 "
        pdb=" N   ASP R 119 "
        pdb=" CA  ASP R 119 "
      ideal   model   delta    sigma   weight residual
     120.38  113.57    6.81 1.37e+00 5.33e-01 2.47e+01
  ... (remaining 12223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4805
       17.88 -    35.76: 419
       35.76 -    53.63: 94
       53.63 -    71.51: 18
       71.51 -    89.39: 7
  Dihedral angle restraints: 5343
    sinusoidal: 2066
      harmonic: 3277
  Sorted by residual:
  dihedral pdb=" CB  CYS S  22 "
           pdb=" SG  CYS S  22 "
           pdb=" SG  CYS S  96 "
           pdb=" CB  CYS S  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.24  -53.24     1      1.00e+01 1.00e-02 3.85e+01
  dihedral pdb=" CA  GLU S 234 "
           pdb=" C   GLU S 234 "
           pdb=" N   TYR S 235 "
           pdb=" CA  TYR S 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.60  -22.40     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  LEU R  74 "
           pdb=" C   LEU R  74 "
           pdb=" N   ILE R  75 "
           pdb=" CA  ILE R  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.35  -21.65     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 5340 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1054
       0.051 -    0.101: 264
       0.101 -    0.152: 44
       0.152 -    0.203: 6
       0.203 -    0.254: 3
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" CA  ARG R 221 "
            pdb=" N   ARG R 221 "
            pdb=" C   ARG R 221 "
            pdb=" CB  ARG R 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  LEU R 282 "
            pdb=" N   LEU R 282 "
            pdb=" C   LEU R 282 "
            pdb=" CB  LEU R 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  ILE R 278 "
            pdb=" N   ILE R 278 "
            pdb=" C   ILE R 278 "
            pdb=" CB  ILE R 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1368 not shown)

  Planarity restraints: 1553
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  UJL R 401 "    0.101 2.00e-02 2.50e+03   8.43e-02 1.24e+02
        pdb=" C5  UJL R 401 "   -0.063 2.00e-02 2.50e+03
        pdb=" C6  UJL R 401 "   -0.015 2.00e-02 2.50e+03
        pdb=" C7  UJL R 401 "    0.021 2.00e-02 2.50e+03
        pdb=" C8  UJL R 401 "    0.111 2.00e-02 2.50e+03
        pdb=" C9  UJL R 401 "   -0.006 2.00e-02 2.50e+03
        pdb=" S1  UJL R 401 "   -0.150 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 209 "    0.017 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   TYR R 209 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   TYR R 209 "    0.023 2.00e-02 2.50e+03
        pdb=" N   TYR R 210 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 286 "    0.018 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   LEU R 286 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   LEU R 286 "    0.022 2.00e-02 2.50e+03
        pdb=" N   TYR R 287 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1550 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1168
        2.75 -     3.29: 8465
        3.29 -     3.83: 13828
        3.83 -     4.36: 16148
        4.36 -     4.90: 28455
  Nonbonded interactions: 68064
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP Y  48 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR R  55 "
            pdb=" OD1 ASN R  58 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" NH1 ARG B  42 "
            pdb=" OE1 GLN B  44 "
     model   vdw
     2.275 3.120
  ... (remaining 68059 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     7.720
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   9023  Z= 0.297
  Angle     :  0.836  10.434  12234  Z= 0.518
  Chirality :  0.047   0.254   1371
  Planarity :  0.006   0.084   1553
  Dihedral  : 14.643  89.390   3222
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  0.42 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.25), residues: 1111
  helix:  0.38 (0.28), residues: 369
  sheet: -0.34 (0.31), residues: 294
  loop : -1.63 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 314 
 TYR   0.016   0.002   TYR R 305 
 PHE   0.027   0.002   PHE S  29 
 TRP   0.053   0.003   TRP S  47 
 HIS   0.012   0.002   HIS R  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 9020)
  covalent geometry    : angle       0.83623 (12228)
  SS BOND              : bond        0.00337 (    3)
  SS BOND              : angle       0.47331 (    6)
  hydrogen bonds       : bond        0.22151 (  378)
  hydrogen bonds       : angle       7.39883 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 258
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ILE cc_start: 0.7880 (mt) cc_final: 0.7342 (mt)
REVERT: A  230 TYR cc_start: 0.6275 (m-80) cc_final: 0.5914 (m-80)
REVERT: R  197 SER cc_start: 0.6763 (t) cc_final: 0.6528 (p)
REVERT: S   27 PHE cc_start: 0.6767 (p90) cc_final: 0.6443 (p90)
  outliers start: 9
  outliers final: 4
  residues processed: 264
  average time/residue: 0.0932
  time to fit residues: 32.7717
Evaluate side-chains
  158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 TYR
Chi-restraints excluded: chain R residue  211 ARG
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain R residue  289 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0970
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 324 HIS
B 259 GLN
R 293 ASN
** S 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.195233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.155226 restraints weight = 11465.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 2.52
r_work: 0.3794 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9023  Z= 0.184
  Angle     :  0.689   8.893  12234  Z= 0.366
  Chirality :  0.046   0.165   1371
  Planarity :  0.005   0.062   1553
  Dihedral  :  5.700  59.713   1254
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 12.43 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.25), residues: 1111
  helix:  0.58 (0.27), residues: 388
  sheet:  0.37 (0.33), residues: 257
  loop : -1.91 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 314 
 TYR   0.019   0.002   TYR S 103 
 PHE   0.017   0.002   PHE B 241 
 TRP   0.029   0.002   TRP S  47 
 HIS   0.007   0.002   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 9020)
  covalent geometry    : angle       0.68871 (12228)
  SS BOND              : bond        0.00526 (    3)
  SS BOND              : angle       0.76408 (    6)
  hydrogen bonds       : bond        0.05593 (  378)
  hydrogen bonds       : angle       5.02659 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  193 LYS cc_start: 0.8243 (mmtm) cc_final: 0.8017 (mttt)
REVERT: A  201 VAL cc_start: 0.8317 (m) cc_final: 0.8095 (t)
REVERT: A  260 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7654 (mtmt)
REVERT: B  124 TYR cc_start: 0.8574 (m-80) cc_final: 0.8236 (m-80)
REVERT: B  226 GLU cc_start: 0.7840 (tp30) cc_final: 0.7612 (mm-30)
REVERT: R  188 VAL cc_start: 0.8348 (m) cc_final: 0.8053 (p)
REVERT: S   34 MET cc_start: 0.7644 (mmm) cc_final: 0.7039 (mmm)
REVERT: Y   50 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8055 (mp)
  outliers start: 20
  outliers final: 10
  residues processed: 179
  average time/residue: 0.0944
  time to fit residues: 22.4883
Evaluate side-chains
  146 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain R residue  289 PHE
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  105 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 83 optimal weight:    7.9990
   chunk 73 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 213 GLN
A 324 HIS
B  75 GLN
R  58 ASN
S 113 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.193557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.153504 restraints weight = 11676.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.70
r_work: 0.3753 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9023  Z= 0.136
  Angle     :  0.589   6.928  12234  Z= 0.311
  Chirality :  0.043   0.163   1371
  Planarity :  0.004   0.050   1553
  Dihedral  :  4.816  43.469   1248
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.75 %
    Favored  : 82.09 %
  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: -0.41 (0.25), residues: 1111
  helix:  0.89 (0.27), residues: 390
  sheet:  0.50 (0.33), residues: 257
  loop : -1.78 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 256 
 TYR   0.018   0.001   TYR A  30 
 PHE   0.018   0.001   PHE B 199 
 TRP   0.023   0.002   TRP S  47 
 HIS   0.007   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9020)
  covalent geometry    : angle       0.58863 (12228)
  SS BOND              : bond        0.00418 (    3)
  SS BOND              : angle       0.76883 (    6)
  hydrogen bonds       : bond        0.04962 (  378)
  hydrogen bonds       : angle       4.63853 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7304 (mpp)
REVERT: A  198 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8233 (ttp)
REVERT: A  206 ASP cc_start: 0.7679 (m-30) cc_final: 0.7450 (p0)
REVERT: A  269 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5757 (mt)
REVERT: B   59 TYR cc_start: 0.8050 (m-80) cc_final: 0.7601 (m-80)
REVERT: B  124 TYR cc_start: 0.8655 (m-80) cc_final: 0.8325 (m-80)
REVERT: B  188 MET cc_start: 0.8365 (mmt) cc_final: 0.7866 (mmt)
REVERT: B  217 MET cc_start: 0.7141 (ttp) cc_final: 0.6833 (ppp)
REVERT: R  188 VAL cc_start: 0.8213 (m) cc_final: 0.7930 (p)
REVERT: S   34 MET cc_start: 0.7646 (mmm) cc_final: 0.7220 (mmm)
REVERT: S  140 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7117 (mtm)
REVERT: Y   50 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8352 (mp)
  outliers start: 30
  outliers final: 15
  residues processed: 168
  average time/residue: 0.0863
  time to fit residues: 19.9203
Evaluate side-chains
  153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain R residue  289 PHE
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  105 SER
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 85 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.182218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140218 restraints weight = 11546.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.72
r_work: 0.3555 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.6944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9023  Z= 0.183
  Angle     :  0.644   8.223  12234  Z= 0.341
  Chirality :  0.045   0.160   1371
  Planarity :  0.005   0.049   1553
  Dihedral  :  5.148  46.182   1248
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 15.91 %
    Favored  : 80.30 %
  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: -0.45 (0.25), residues: 1111
  helix:  0.98 (0.27), residues: 382
  sheet:  0.49 (0.32), residues: 265
  loop : -1.92 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 256 
 TYR   0.020   0.002   TYR A  30 
 PHE   0.017   0.002   PHE S  29 
 TRP   0.026   0.002   TRP S  47 
 HIS   0.006   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 9020)
  covalent geometry    : angle       0.64336 (12228)
  SS BOND              : bond        0.00478 (    3)
  SS BOND              : angle       0.99303 (    6)
  hydrogen bonds       : bond        0.06053 (  378)
  hydrogen bonds       : angle       4.85160 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7167 (mpp)
REVERT: A  269 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.5809 (mt)
REVERT: A  281 GLU cc_start: 0.6939 (tp30) cc_final: 0.6171 (tp30)
REVERT: B   59 TYR cc_start: 0.8366 (m-80) cc_final: 0.7770 (m-80)
REVERT: B  124 TYR cc_start: 0.8684 (m-80) cc_final: 0.8366 (m-80)
REVERT: B  138 GLU cc_start: 0.8834 (tt0) cc_final: 0.8624 (tt0)
REVERT: B  234 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6407 (m-80)
REVERT: R   86 ARG cc_start: 0.7269 (mtt90) cc_final: 0.6887 (mpt180)
REVERT: R  188 VAL cc_start: 0.8017 (m) cc_final: 0.7773 (p)
REVERT: S   34 MET cc_start: 0.7862 (mmm) cc_final: 0.7557 (mmm)
REVERT: S   77 ASN cc_start: 0.6406 (m-40) cc_final: 0.5836 (p0)
REVERT: Y   50 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8387 (mp)
  outliers start: 36
  outliers final: 18
  residues processed: 181
  average time/residue: 0.0851
  time to fit residues: 21.3277
Evaluate side-chains
  159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  289 PHE
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 99 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 10 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 213 GLN
B 340 ASN
R  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.184814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.144570 restraints weight = 11613.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.90
r_work: 0.3586 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.7188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9023  Z= 0.122
  Angle     :  0.563   7.690  12234  Z= 0.295
  Chirality :  0.042   0.161   1371
  Planarity :  0.004   0.044   1553
  Dihedral  :  4.574  41.956   1244
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.65 %
    Favored  : 80.19 %
  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: -0.25 (0.25), residues: 1111
  helix:  1.21 (0.27), residues: 383
  sheet:  0.46 (0.32), residues: 270
  loop : -1.81 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 256 
 TYR   0.016   0.001   TYR A  30 
 PHE   0.020   0.001   PHE B 199 
 TRP   0.024   0.002   TRP S  47 
 HIS   0.004   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9020)
  covalent geometry    : angle       0.56332 (12228)
  SS BOND              : bond        0.00329 (    3)
  SS BOND              : angle       0.79029 (    6)
  hydrogen bonds       : bond        0.04568 (  378)
  hydrogen bonds       : angle       4.44756 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7583 (mpp)
REVERT: A  269 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.5912 (mt)
REVERT: A  281 GLU cc_start: 0.6836 (tp30) cc_final: 0.6062 (tp30)
REVERT: A  359 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8085 (mm-30)
REVERT: B   59 TYR cc_start: 0.8165 (m-80) cc_final: 0.7702 (m-80)
REVERT: B  124 TYR cc_start: 0.8654 (m-80) cc_final: 0.8275 (m-80)
REVERT: R  188 VAL cc_start: 0.8065 (m) cc_final: 0.7824 (p)
REVERT: S   34 MET cc_start: 0.7699 (mmm) cc_final: 0.7455 (mmm)
REVERT: S   77 ASN cc_start: 0.6266 (m-40) cc_final: 0.5822 (p0)
REVERT: Y   50 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8018 (mp)
  outliers start: 30
  outliers final: 20
  residues processed: 168
  average time/residue: 0.0890
  time to fit residues: 20.4007
Evaluate side-chains
  151 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  252 ILE
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  289 PHE
Chi-restraints excluded: chain R residue  304 PHE
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   chunk 39 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 259 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.186971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.148091 restraints weight = 11510.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.60
r_work: 0.3633 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.7432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9023  Z= 0.110
  Angle     :  0.554   7.881  12234  Z= 0.287
  Chirality :  0.041   0.159   1371
  Planarity :  0.004   0.044   1553
  Dihedral  :  4.363  41.449   1244
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.76 %
    Favored  : 78.71 %
  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: -0.00 (0.25), residues: 1111
  helix:  1.54 (0.27), residues: 373
  sheet:  0.43 (0.32), residues: 269
  loop : -1.58 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 314 
 TYR   0.013   0.001   TYR A  30 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.022   0.002   TRP S  47 
 HIS   0.003   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9020)
  covalent geometry    : angle       0.55416 (12228)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.64151 (    6)
  hydrogen bonds       : bond        0.04070 (  378)
  hydrogen bonds       : angle       4.27558 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7338 (mpp)
REVERT: A  281 GLU cc_start: 0.6698 (tp30) cc_final: 0.5910 (tp30)
REVERT: A  282 PHE cc_start: 0.5018 (t80) cc_final: 0.4745 (t80)
REVERT: A  359 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8185 (mm-30)
REVERT: B   59 TYR cc_start: 0.8269 (m-80) cc_final: 0.7707 (m-80)
REVERT: B  124 TYR cc_start: 0.8715 (m-80) cc_final: 0.8277 (m-80)
REVERT: B  172 GLU cc_start: 0.7780 (tp30) cc_final: 0.7487 (tm-30)
REVERT: B  227 SER cc_start: 0.9049 (m) cc_final: 0.8770 (t)
REVERT: R   82 ARG cc_start: 0.7608 (tmm-80) cc_final: 0.7326 (tmm-80)
REVERT: R   86 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6782 (mpt180)
REVERT: R  188 VAL cc_start: 0.8067 (m) cc_final: 0.7812 (p)
REVERT: S   34 MET cc_start: 0.7757 (mmm) cc_final: 0.7479 (mmm)
REVERT: S   77 ASN cc_start: 0.6170 (m-40) cc_final: 0.5690 (p0)
REVERT: S   93 MET cc_start: 0.6010 (tpt) cc_final: 0.5761 (mmm)
REVERT: Y   50 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8336 (mp)
  outliers start: 24
  outliers final: 16
  residues processed: 163
  average time/residue: 0.0947
  time to fit residues: 21.1624
Evaluate side-chains
  150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  289 PHE
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:   50.0000
   chunk 84 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.9786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.186599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.144647 restraints weight = 11595.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.86
r_work: 0.3597 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.7633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9023  Z= 0.110
  Angle     :  0.548   7.916  12234  Z= 0.283
  Chirality :  0.041   0.159   1371
  Planarity :  0.004   0.044   1553
  Dihedral  :  4.297  41.004   1244
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.28 %
    Favored  : 78.61 %
  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:  0.16 (0.25), residues: 1111
  helix:  1.74 (0.27), residues: 372
  sheet:  0.45 (0.32), residues: 269
  loop : -1.50 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 314 
 TYR   0.015   0.001   TYR A  30 
 PHE   0.012   0.001   PHE A 189 
 TRP   0.021   0.002   TRP S  47 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9020)
  covalent geometry    : angle       0.54747 (12228)
  SS BOND              : bond        0.00329 (    3)
  SS BOND              : angle       0.60954 (    6)
  hydrogen bonds       : bond        0.04102 (  378)
  hydrogen bonds       : angle       4.23468 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7295 (mpp)
REVERT: A  269 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5765 (mt)
REVERT: A  281 GLU cc_start: 0.6707 (tp30) cc_final: 0.5932 (tp30)
REVERT: A  300 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7730 (mmm160)
REVERT: A  359 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8101 (mm-30)
REVERT: B   59 TYR cc_start: 0.8157 (m-80) cc_final: 0.7620 (m-80)
REVERT: B  124 TYR cc_start: 0.8630 (m-80) cc_final: 0.8174 (m-80)
REVERT: B  217 MET cc_start: 0.7837 (ptm) cc_final: 0.7459 (ppp)
REVERT: B  227 SER cc_start: 0.8970 (m) cc_final: 0.8676 (t)
REVERT: R   82 ARG cc_start: 0.7508 (tmm-80) cc_final: 0.7291 (tmm-80)
REVERT: R  188 VAL cc_start: 0.8039 (m) cc_final: 0.7786 (p)
REVERT: S   34 MET cc_start: 0.7648 (mmm) cc_final: 0.7310 (mmm)
REVERT: S   77 ASN cc_start: 0.6237 (m-40) cc_final: 0.5666 (p0)
REVERT: Y   50 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8396 (mp)
  outliers start: 20
  outliers final: 14
  residues processed: 163
  average time/residue: 0.1049
  time to fit residues: 22.9122
Evaluate side-chains
  153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  289 PHE
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 80 optimal weight:    9.9990
   chunk 86 optimal weight:    0.6980
   chunk 97 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 101 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 96 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.187141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.147003 restraints weight = 11829.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.82
r_work: 0.3694 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.7915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9023  Z= 0.160
  Angle     :  0.606   8.833  12234  Z= 0.316
  Chirality :  0.043   0.157   1371
  Planarity :  0.004   0.049   1553
  Dihedral  :  4.629  41.974   1244
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.28 %
    Favored  : 77.98 %
  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:  0.05 (0.25), residues: 1111
  helix:  1.63 (0.27), residues: 373
  sheet:  0.31 (0.32), residues: 270
  loop : -1.49 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 314 
 TYR   0.022   0.001   TYR A  30 
 PHE   0.014   0.001   PHE S  29 
 TRP   0.023   0.002   TRP S  47 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9020)
  covalent geometry    : angle       0.60580 (12228)
  SS BOND              : bond        0.00455 (    3)
  SS BOND              : angle       0.81399 (    6)
  hydrogen bonds       : bond        0.05248 (  378)
  hydrogen bonds       : angle       4.51636 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7386 (mpp)
REVERT: A  269 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5719 (mt)
REVERT: A  300 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7788 (tpp80)
REVERT: A  324 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8481 (p90)
REVERT: B   59 TYR cc_start: 0.8191 (m-80) cc_final: 0.7729 (m-80)
REVERT: B  124 TYR cc_start: 0.8609 (m-80) cc_final: 0.8289 (m-80)
REVERT: B  227 SER cc_start: 0.9075 (m) cc_final: 0.8819 (t)
REVERT: R   82 ARG cc_start: 0.7644 (tmm-80) cc_final: 0.7438 (tmm-80)
REVERT: R   86 ARG cc_start: 0.7236 (mtt90) cc_final: 0.6588 (mpt180)
REVERT: R  188 VAL cc_start: 0.7976 (m) cc_final: 0.7766 (p)
REVERT: R  189 SER cc_start: 0.8449 (m) cc_final: 0.8097 (p)
REVERT: S   34 MET cc_start: 0.7870 (mmm) cc_final: 0.7568 (mmm)
REVERT: Y   50 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8440 (mp)
  outliers start: 26
  outliers final: 17
  residues processed: 166
  average time/residue: 0.1060
  time to fit residues: 23.7487
Evaluate side-chains
  159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  289 PHE
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.191259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.151283 restraints weight = 11875.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 2.63
r_work: 0.3728 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.8036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9023  Z= 0.112
  Angle     :  0.562   8.277  12234  Z= 0.290
  Chirality :  0.041   0.159   1371
  Planarity :  0.004   0.054   1553
  Dihedral  :  4.313  40.940   1244
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.34 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.21 (0.26), residues: 1111
  helix:  1.81 (0.27), residues: 372
  sheet:  0.39 (0.32), residues: 269
  loop : -1.44 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 314 
 TYR   0.013   0.001   TYR R 287 
 PHE   0.012   0.001   PHE S  29 
 TRP   0.020   0.002   TRP S  47 
 HIS   0.003   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9020)
  covalent geometry    : angle       0.56204 (12228)
  SS BOND              : bond        0.00322 (    3)
  SS BOND              : angle       0.54691 (    6)
  hydrogen bonds       : bond        0.04009 (  378)
  hydrogen bonds       : angle       4.25970 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7260 (mpp)
REVERT: A  269 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5686 (mt)
REVERT: A  300 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7768 (tpp80)
REVERT: A  314 ARG cc_start: 0.7448 (ttm110) cc_final: 0.7147 (ttp80)
REVERT: A  324 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.8414 (p90)
REVERT: B   59 TYR cc_start: 0.7926 (m-80) cc_final: 0.7706 (m-80)
REVERT: B  124 TYR cc_start: 0.8621 (m-80) cc_final: 0.8256 (m-80)
REVERT: B  217 MET cc_start: 0.8085 (ptm) cc_final: 0.7715 (ppp)
REVERT: B  227 SER cc_start: 0.9071 (m) cc_final: 0.8801 (t)
REVERT: R  188 VAL cc_start: 0.7959 (m) cc_final: 0.7724 (p)
REVERT: R  189 SER cc_start: 0.8356 (m) cc_final: 0.8007 (p)
REVERT: S   34 MET cc_start: 0.7738 (mmm) cc_final: 0.7497 (mmm)
REVERT: Y   50 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8453 (mp)
  outliers start: 20
  outliers final: 15
  residues processed: 162
  average time/residue: 0.1071
  time to fit residues: 23.3579
Evaluate side-chains
  155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain S residue   47 TRP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 106 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 5 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 100 optimal weight:    0.3980
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
A 213 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.192962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.151665 restraints weight = 11884.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 2.82
r_work: 0.3746 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.8152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9023  Z= 0.108
  Angle     :  0.567   8.928  12234  Z= 0.292
  Chirality :  0.041   0.159   1371
  Planarity :  0.004   0.053   1553
  Dihedral  :  4.054  35.179   1242
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.76 %
    Favored  : 77.24 %
  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:  0.32 (0.26), residues: 1111
  helix:  1.94 (0.27), residues: 373
  sheet:  0.41 (0.32), residues: 271
  loop : -1.37 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 314 
 TYR   0.013   0.001   TYR R 287 
 PHE   0.019   0.001   PHE B 199 
 TRP   0.019   0.001   TRP S  47 
 HIS   0.003   0.001   HIS R  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9020)
  covalent geometry    : angle       0.56695 (12228)
  SS BOND              : bond        0.00321 (    3)
  SS BOND              : angle       0.64727 (    6)
  hydrogen bonds       : bond        0.03763 (  378)
  hydrogen bonds       : angle       4.18883 ( 1083)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7203 (mpp)
REVERT: A  269 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5734 (mt)
REVERT: A  300 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7729 (mmm160)
REVERT: A  314 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7154 (ttp80)
REVERT: A  324 HIS cc_start: 0.8848 (OUTLIER) cc_final: 0.8362 (p90)
REVERT: B   59 TYR cc_start: 0.7781 (m-80) cc_final: 0.7565 (m-80)
REVERT: B  124 TYR cc_start: 0.8592 (m-80) cc_final: 0.8191 (m-80)
REVERT: B  227 SER cc_start: 0.9075 (m) cc_final: 0.8778 (t)
REVERT: R  188 VAL cc_start: 0.7962 (m) cc_final: 0.7734 (p)
REVERT: R  189 SER cc_start: 0.8374 (m) cc_final: 0.8024 (p)
REVERT: S   34 MET cc_start: 0.7721 (mmm) cc_final: 0.7441 (mmm)
REVERT: Y   50 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8460 (mp)
  outliers start: 19
  outliers final: 13
  residues processed: 163
  average time/residue: 0.1101
  time to fit residues: 24.3668
Evaluate side-chains
  161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain Y residue   17 GLU
Chi-restraints excluded: chain Y residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 86 optimal weight:    0.4980
   chunk 107 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.0586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.186933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.146864 restraints weight = 11885.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 2.82
r_work: 0.3664 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.8241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9023  Z= 0.164
  Angle     :  0.625   8.591  12234  Z= 0.326
  Chirality :  0.043   0.156   1371
  Planarity :  0.004   0.050   1553
  Dihedral  :  4.459  42.286   1242
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.86 %
    Favored  : 76.82 %
  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:  0.18 (0.26), residues: 1111
  helix:  1.77 (0.27), residues: 379
  sheet:  0.27 (0.31), residues: 272
  loop : -1.42 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 314 
 TYR   0.023   0.002   TYR A  30 
 PHE   0.021   0.002   PHE B 199 
 TRP   0.061   0.003   TRP S  47 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9020)
  covalent geometry    : angle       0.62510 (12228)
  SS BOND              : bond        0.00453 (    3)
  SS BOND              : angle       0.80592 (    6)
  hydrogen bonds       : bond        0.05252 (  378)
  hydrogen bonds       : angle       4.49095 ( 1083)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2142.09 seconds
wall clock time: 37 minutes 21.66 seconds (2241.66 seconds total)