Starting phenix.real_space_refine
on Wed Sep 17 16:23:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3p_62024/09_2025/9k3p_62024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3p_62024/09_2025/9k3p_62024.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k3p_62024/09_2025/9k3p_62024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3p_62024/09_2025/9k3p_62024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3p_62024/09_2025/9k3p_62024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3p_62024/09_2025/9k3p_62024.cif"
  }
  resolution = 2.98
  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=   0.024
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      65      5.16       5
     C    5958      2.51       5
     N    1625      2.21       5
     O    1768      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9416
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1880
          Classifications: {'peptide': 257}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 250}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "A"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1932
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2517
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "G"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 386
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "N"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 930
          Classifications: {'peptide': 123}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "S"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
  Time building chain proxies: 1.98, per 1000 atoms: 0.21
  Number of scatterers: 9416
  At special positions: 0
  Unit cell: (84.609, 134.946, 126.378, 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      65     16.00
     O    1768      8.00
     N    1625      7.00
     C    5958      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 267 " - pdb=" SG  CYS R 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    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=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 275.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 18 sheets defined
      34.4% alpha, 24.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'R' and resid 43 through 66
    Processing helix  chain 'R' and resid 67 through 70
    Processing helix  chain 'R' and resid 71 through 101
      removed outlier: 3.631A  pdb=" N   THR R  95 " --> pdb=" O   ASN R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 104
      No H-bonds generated for 'chain 'R' and resid 102 through 104'
    Processing helix  chain 'R' and resid 109 through 148
      removed outlier: 3.708A  pdb=" N   ASN R 118 " --> pdb=" O   GLN R 114 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET R 128 " --> pdb=" O   THR R 124 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   CYS R 133 " --> pdb=" O   LEU R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 155
    Processing helix  chain 'R' and resid 157 through 180
    Processing helix  chain 'R' and resid 190 through 209
      removed outlier: 4.028A  pdb=" N   LEU R 197 " --> pdb=" O   VAL R 193 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU R 206 " --> pdb=" O   LEU R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 224
      removed outlier: 3.874A  pdb=" N   LEU R 224 " --> pdb=" O   GLY R 220 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 264
      removed outlier: 4.468A  pdb=" N   PHE R 250 " --> pdb=" O   LEU R 246 " (cutoff:3.500A)
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 276 through 278
      No H-bonds generated for 'chain 'R' and resid 276 through 278'
    Processing helix  chain 'R' and resid 279 through 289
    Processing helix  chain 'R' and resid 289 through 299
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 302 through 308
      removed outlier: 3.671A  pdb=" N   THR R 308 " --> pdb=" O   GLU R 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 38
      removed outlier: 3.581A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LYS A  24 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLN A  29 " --> pdb=" O   MET A  25 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 252 through 278
      removed outlier: 4.131A  pdb=" N   GLN A 267 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.640A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 4.061A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.776A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'G' and resid 11 through 24
      removed outlier: 3.734A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 43
      removed outlier: 3.809A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.258A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 74 through 77
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.904A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41
      removed outlier: 6.803A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208
      removed outlier: 7.220A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 208
      removed outlier: 7.220A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 52
      removed outlier: 4.109A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.592A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.323A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.756A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.708A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.147A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.816A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 6 through 7
      removed outlier: 5.501A  pdb=" N   GLY N  16 " --> pdb=" O   SER N  85 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.596A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN N  39 " --> pdb=" O   VAL N  93 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL N  37 " --> pdb=" O   TYR N  95 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 3 through 5
      removed outlier: 3.647A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 58 through 60
      removed outlier: 5.377A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 58 through 60
      removed outlier: 5.377A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 146 through 148
      removed outlier: 5.973A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR S 243 " --> pdb=" O   TYR S 227 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'S' and resid 155 through 160
      removed outlier: 3.584A  pdb=" N   VAL S 155 " --> pdb=" O   ILE S 216 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'S' and resid 185 through 189
      removed outlier: 5.794A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    439 hydrogen bonds defined for protein.
    1215 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: 1.37

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3089
        1.34 -     1.46: 1988
        1.46 -     1.58: 4439
        1.58 -     1.70: 0
        1.70 -     1.81: 91
  Bond restraints: 9607
  Sorted by residual:
  bond pdb=" CB  ILE B  80 "
       pdb=" CG2 ILE B  80 "
    ideal  model  delta    sigma   weight residual
    1.521  1.434  0.087 3.30e-02 9.18e+02 7.02e+00
  bond pdb=" CG1 ILE A 382 "
       pdb=" CD1 ILE A 382 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.21e+00
  bond pdb=" C   TRP B  99 "
       pdb=" N   VAL B 100 "
    ideal  model  delta    sigma   weight residual
    1.333  1.317  0.016 1.20e-02 6.94e+03 1.77e+00
  bond pdb=" N   PRO G  60 "
       pdb=" CA  PRO G  60 "
    ideal  model  delta    sigma   weight residual
    1.474  1.465  0.009 7.40e-03 1.83e+04 1.41e+00
  bond pdb=" CA  ASP A 343 "
       pdb=" C   ASP A 343 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.016 1.35e-02 5.49e+03 1.38e+00
  ... (remaining 9602 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 12473
        1.59 -     3.18: 465
        3.18 -     4.77: 77
        4.77 -     6.36: 13
        6.36 -     7.96: 5
  Bond angle restraints: 13033
  Sorted by residual:
  angle pdb=" C   GLU A 344 "
        pdb=" CA  GLU A 344 "
        pdb=" CB  GLU A 344 "
      ideal   model   delta    sigma   weight residual
     110.31  102.67    7.64 2.09e+00 2.29e-01 1.34e+01
  angle pdb=" N   ALA N  92 "
        pdb=" CA  ALA N  92 "
        pdb=" C   ALA N  92 "
      ideal   model   delta    sigma   weight residual
     107.88  112.95   -5.07 1.41e+00 5.03e-01 1.30e+01
  angle pdb=" CA  MET B 262 "
        pdb=" CB  MET B 262 "
        pdb=" CG  MET B 262 "
      ideal   model   delta    sigma   weight residual
     114.10  120.19   -6.09 2.00e+00 2.50e-01 9.26e+00
  angle pdb=" N   PHE A 345 "
        pdb=" CA  PHE A 345 "
        pdb=" C   PHE A 345 "
      ideal   model   delta    sigma   weight residual
     113.23  109.76    3.47 1.24e+00 6.50e-01 7.85e+00
  angle pdb=" C   GLU R 269 "
        pdb=" N   HIS R 270 "
        pdb=" CA  HIS R 270 "
      ideal   model   delta    sigma   weight residual
     122.56  126.69   -4.13 1.58e+00 4.01e-01 6.83e+00
  ... (remaining 13028 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 5152
       17.15 -    34.30: 445
       34.30 -    51.45: 70
       51.45 -    68.60: 17
       68.60 -    85.75: 12
  Dihedral angle restraints: 5696
    sinusoidal: 2144
      harmonic: 3552
  Sorted by residual:
  dihedral pdb=" CB  CYS R 267 "
           pdb=" SG  CYS R 267 "
           pdb=" SG  CYS R 273 "
           pdb=" CB  CYS R 273 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.01  -83.01     1      1.00e+01 1.00e-02 8.43e+01
  dihedral pdb=" CA  ILE R 180 "
           pdb=" C   ILE R 180 "
           pdb=" N   ALA R 181 "
           pdb=" CA  ALA R 181 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.73  -29.27     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  TYR R 182 "
           pdb=" C   TYR R 182 "
           pdb=" N   TYR R 183 "
           pdb=" CA  TYR R 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.87  -23.13     0      5.00e+00 4.00e-02 2.14e+01
  ... (remaining 5693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 978
       0.041 -    0.082: 363
       0.082 -    0.123: 120
       0.123 -    0.163: 22
       0.163 -    0.204: 2
  Chirality restraints: 1485
  Sorted by residual:
  chirality pdb=" CA  TRP S  47 "
            pdb=" N   TRP S  47 "
            pdb=" C   TRP S  47 "
            pdb=" CB  TRP S  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  PHE A 345 "
            pdb=" N   PHE A 345 "
            pdb=" C   PHE A 345 "
            pdb=" CB  PHE A 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.96e-01
  chirality pdb=" CA  TRP B  82 "
            pdb=" N   TRP B  82 "
            pdb=" C   TRP B  82 "
            pdb=" CB  TRP B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 1482 not shown)

  Planarity restraints: 1665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S  47 "   -0.037 2.00e-02 2.50e+03   3.12e-02 2.44e+01
        pdb=" CG  TRP S  47 "    0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP S  47 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP S  47 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP S  47 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP S  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP S  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S  47 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP S  47 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 332 "   -0.028 2.00e-02 2.50e+03   2.24e-02 1.25e+01
        pdb=" CG  TRP B 332 "    0.060 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 332 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 332 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 332 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 332 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 332 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 332 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R 267 "    0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO R 268 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO R 268 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 268 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1662 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 196
        2.66 -     3.22: 9219
        3.22 -     3.78: 15008
        3.78 -     4.34: 20414
        4.34 -     4.90: 33423
  Nonbonded interactions: 78260
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 330 "
            pdb=" OG1 THR A 335 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" O   GLY R  49 "
            pdb=" OG  SER R  88 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" NE  ARG S  38 "
            pdb=" OE2 GLU S  46 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" NE  ARG B 314 "
     model   vdw
     2.154 3.120
  ... (remaining 78255 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.710
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6624
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   0.087   9612  Z= 0.214
  Angle     :  0.727   7.956  13043  Z= 0.413
  Chirality :  0.047   0.204   1485
  Planarity :  0.004   0.056   1665
  Dihedral  : 13.633  85.748   3393
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.80 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.24), residues: 1207
  helix: -0.53 (0.26), residues: 383
  sheet: -1.50 (0.31), residues: 294
  loop : -1.56 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 333 
 TYR   0.023   0.002   TYR B  85 
 PHE   0.029   0.003   PHE R 134 
 TRP   0.082   0.004   TRP S  47 
 HIS   0.016   0.002   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 9607)
  covalent geometry    : angle       0.72650 (13033)
  SS BOND              : bond        0.00219 (    5)
  SS BOND              : angle       1.14610 (   10)
  hydrogen bonds       : bond        0.22179 (  422)
  hydrogen bonds       : angle       8.90578 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.6942 (m-30) cc_final: 0.5995 (t0)
REVERT: A   28 LYS cc_start: 0.7582 (mtmm) cc_final: 0.7315 (mtmm)
REVERT: A  216 LYS cc_start: 0.7319 (mppt) cc_final: 0.7012 (mppt)
REVERT: A  340 PHE cc_start: 0.6344 (t80) cc_final: 0.6040 (t80)
REVERT: B   69 LEU cc_start: 0.7047 (mt) cc_final: 0.6846 (mt)
REVERT: G   22 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7498 (mt-10)
REVERT: N   34 MET cc_start: 0.6633 (mmt) cc_final: 0.5911 (mmt)
  outliers start: 1
  outliers final: 2
  residues processed: 237
  average time/residue: 0.4701
  time to fit residues: 119.6431
Evaluate side-chains
  204 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  245 ILE
Chi-restraints excluded: chain A residue  331 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.152094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.131812 restraints weight = 15685.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.55
r_work: 0.3848 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9612  Z= 0.194
  Angle     :  0.704   6.965  13043  Z= 0.377
  Chirality :  0.046   0.160   1485
  Planarity :  0.005   0.045   1665
  Dihedral  :  5.848  72.979   1336
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.50 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.24), residues: 1207
  helix: -0.07 (0.26), residues: 385
  sheet: -1.28 (0.30), residues: 310
  loop : -1.65 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 389 
 TYR   0.018   0.002   TYR B  85 
 PHE   0.019   0.002   PHE N  29 
 TRP   0.034   0.003   TRP S  47 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 9607)
  covalent geometry    : angle       0.70360 (13033)
  SS BOND              : bond        0.00407 (    5)
  SS BOND              : angle       0.91017 (   10)
  hydrogen bonds       : bond        0.04797 (  422)
  hydrogen bonds       : angle       6.29600 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 224
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7501 (mtmm)
REVERT: A  216 LYS cc_start: 0.7605 (mppt) cc_final: 0.7134 (mppt)
REVERT: A  318 TYR cc_start: 0.5908 (t80) cc_final: 0.5029 (t80)
REVERT: A  340 PHE cc_start: 0.6895 (t80) cc_final: 0.6511 (t80)
REVERT: A  373 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7363 (tpp-160)
REVERT: B    8 ARG cc_start: 0.7129 (mtm110) cc_final: 0.6595 (mtt90)
REVERT: B   19 ARG cc_start: 0.7323 (ttm110) cc_final: 0.6801 (ttp-110)
REVERT: B  217 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6961 (pp-130)
REVERT: B  336 LEU cc_start: 0.8108 (tp) cc_final: 0.7905 (tm)
REVERT: G   17 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: N   34 MET cc_start: 0.7038 (mmt) cc_final: 0.6398 (mmp)
REVERT: N   51 ILE cc_start: 0.8106 (tt) cc_final: 0.7690 (pt)
  outliers start: 21
  outliers final: 9
  residues processed: 228
  average time/residue: 0.5307
  time to fit residues: 129.4446
Evaluate side-chains
  228 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 218
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 105 optimal weight:    0.2980
   chunk 98 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
B  88 ASN
N  31 ASN
S 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.153184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.133476 restraints weight = 15786.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.52
r_work: 0.3847 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9612  Z= 0.177
  Angle     :  0.668   8.067  13043  Z= 0.353
  Chirality :  0.046   0.161   1485
  Planarity :  0.004   0.044   1665
  Dihedral  :  5.258  28.505   1332
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.20 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.24), residues: 1207
  helix:  0.19 (0.27), residues: 384
  sheet: -1.14 (0.30), residues: 312
  loop : -1.64 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 314 
 TYR   0.011   0.002   TYR R  74 
 PHE   0.016   0.002   PHE N  29 
 TRP   0.020   0.003   TRP S  47 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9607)
  covalent geometry    : angle       0.66717 (13033)
  SS BOND              : bond        0.00195 (    5)
  SS BOND              : angle       1.13355 (   10)
  hydrogen bonds       : bond        0.04273 (  422)
  hydrogen bonds       : angle       5.88890 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 226
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  287 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6531 (mt)
REVERT: A   16 ASP cc_start: 0.6920 (m-30) cc_final: 0.5919 (t0)
REVERT: A   25 MET cc_start: 0.6911 (mpp) cc_final: 0.6495 (mpp)
REVERT: A   28 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7504 (mtmm)
REVERT: A  216 LYS cc_start: 0.7608 (mppt) cc_final: 0.7226 (mppt)
REVERT: A  284 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8038 (p)
REVERT: A  340 PHE cc_start: 0.6706 (t80) cc_final: 0.6505 (t80)
REVERT: A  344 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6742 (mm-30)
REVERT: A  381 ASP cc_start: 0.7660 (m-30) cc_final: 0.7161 (m-30)
REVERT: A  391 TYR cc_start: 0.7779 (m-10) cc_final: 0.6970 (m-10)
REVERT: A  392 GLU cc_start: 0.7697 (mp0) cc_final: 0.7417 (mp0)
REVERT: B    8 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6590 (mtt90)
REVERT: B   90 VAL cc_start: 0.7838 (t) cc_final: 0.7584 (t)
REVERT: B  100 VAL cc_start: 0.8792 (t) cc_final: 0.8544 (m)
REVERT: B  217 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6970 (pp-130)
REVERT: B  332 TRP cc_start: 0.6838 (m-10) cc_final: 0.6604 (m-10)
REVERT: G   17 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7576 (mm-30)
REVERT: G   22 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7463 (mt-10)
REVERT: N   34 MET cc_start: 0.7019 (mmt) cc_final: 0.6592 (mmp)
REVERT: N   51 ILE cc_start: 0.8125 (tt) cc_final: 0.7637 (pt)
REVERT: N   83 MET cc_start: 0.6257 (mmp) cc_final: 0.6015 (mmp)
  outliers start: 32
  outliers final: 18
  residues processed: 231
  average time/residue: 0.4871
  time to fit residues: 120.9458
Evaluate side-chains
  239 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 217
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 CYS
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue  106 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 6 optimal weight:   30.0000
   chunk 32 optimal weight:    0.1980
   chunk 16 optimal weight:    0.0980
   chunk 116 optimal weight:    0.7980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  88 ASN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.155521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.135283 restraints weight = 15805.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 2.58
r_work: 0.3913 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9612  Z= 0.148
  Angle     :  0.648   8.063  13043  Z= 0.340
  Chirality :  0.044   0.162   1485
  Planarity :  0.004   0.044   1665
  Dihedral  :  5.064  29.962   1332
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.20 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.25), residues: 1207
  helix:  0.49 (0.27), residues: 385
  sheet: -1.03 (0.29), residues: 312
  loop : -1.54 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 389 
 TYR   0.011   0.001   TYR R  74 
 PHE   0.023   0.002   PHE R 134 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9607)
  covalent geometry    : angle       0.64768 (13033)
  SS BOND              : bond        0.00266 (    5)
  SS BOND              : angle       0.91935 (   10)
  hydrogen bonds       : bond        0.03923 (  422)
  hydrogen bonds       : angle       5.52080 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 223
  time to evaluate  : 0.352 
Fit side-chains
REVERT: R  287 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6438 (mt)
REVERT: A   25 MET cc_start: 0.6878 (mpp) cc_final: 0.6417 (mpp)
REVERT: A   28 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7493 (mtmm)
REVERT: A  216 LYS cc_start: 0.7616 (mppt) cc_final: 0.7205 (mppt)
REVERT: A  284 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.8023 (p)
REVERT: A  331 ASP cc_start: 0.6763 (t70) cc_final: 0.6538 (t0)
REVERT: A  340 PHE cc_start: 0.6756 (t80) cc_final: 0.6467 (t80)
REVERT: A  344 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6376 (mm-30)
REVERT: A  391 TYR cc_start: 0.7722 (m-10) cc_final: 0.6883 (m-10)
REVERT: A  392 GLU cc_start: 0.7696 (mp0) cc_final: 0.7379 (mp0)
REVERT: B    8 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6652 (mtt90)
REVERT: B  100 VAL cc_start: 0.8746 (t) cc_final: 0.8437 (m)
REVERT: G   17 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7560 (mm-30)
REVERT: G   21 MET cc_start: 0.7636 (ttp) cc_final: 0.7188 (ppp)
REVERT: G   22 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7290 (mt-10)
REVERT: N   34 MET cc_start: 0.6982 (mmt) cc_final: 0.6547 (mmp)
REVERT: N   51 ILE cc_start: 0.7981 (tt) cc_final: 0.7507 (pt)
REVERT: N   83 MET cc_start: 0.6215 (mmp) cc_final: 0.5998 (mmp)
REVERT: N  104 THR cc_start: 0.8386 (p) cc_final: 0.8051 (t)
REVERT: S  138 ILE cc_start: 0.6010 (OUTLIER) cc_final: 0.5800 (mm)
  outliers start: 30
  outliers final: 17
  residues processed: 233
  average time/residue: 0.4939
  time to fit residues: 123.7350
Evaluate side-chains
  238 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue  138 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 47 optimal weight:    0.4980
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
B  75 GLN
S 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.151728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.131741 restraints weight = 15854.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.54
r_work: 0.3847 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9612  Z= 0.194
  Angle     :  0.679   9.569  13043  Z= 0.356
  Chirality :  0.045   0.157   1485
  Planarity :  0.004   0.040   1665
  Dihedral  :  5.165  29.404   1332
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.50 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.24), residues: 1207
  helix:  0.63 (0.27), residues: 380
  sheet: -0.97 (0.30), residues: 303
  loop : -1.60 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 389 
 TYR   0.011   0.002   TYR A 318 
 PHE   0.021   0.002   PHE G  61 
 TRP   0.035   0.003   TRP B  82 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 9607)
  covalent geometry    : angle       0.67842 (13033)
  SS BOND              : bond        0.00284 (    5)
  SS BOND              : angle       1.07080 (   10)
  hydrogen bonds       : bond        0.04042 (  422)
  hydrogen bonds       : angle       5.45058 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 217
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   25 MET cc_start: 0.6931 (mpp) cc_final: 0.6489 (mpp)
REVERT: A   28 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7540 (mtmm)
REVERT: A   58 LYS cc_start: 0.7669 (tppt) cc_final: 0.7336 (tmmt)
REVERT: A  216 LYS cc_start: 0.7625 (mppt) cc_final: 0.7231 (mppt)
REVERT: A  284 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8050 (p)
REVERT: A  318 TYR cc_start: 0.5849 (t80) cc_final: 0.5430 (t80)
REVERT: A  340 PHE cc_start: 0.6738 (t80) cc_final: 0.6358 (t80)
REVERT: A  344 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6534 (mm-30)
REVERT: A  392 GLU cc_start: 0.7664 (mp0) cc_final: 0.7331 (mp0)
REVERT: B    8 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6720 (mtt90)
REVERT: B   43 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8110 (mp)
REVERT: B  100 VAL cc_start: 0.8717 (t) cc_final: 0.8461 (m)
REVERT: B  269 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8358 (OUTLIER)
REVERT: B  336 LEU cc_start: 0.8174 (tp) cc_final: 0.7967 (mt)
REVERT: G   17 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7573 (mm-30)
REVERT: G   22 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7435 (mt-10)
REVERT: N   34 MET cc_start: 0.7041 (mmt) cc_final: 0.6482 (mmp)
REVERT: N   51 ILE cc_start: 0.8079 (tt) cc_final: 0.7605 (pt)
REVERT: N   83 MET cc_start: 0.6220 (mmp) cc_final: 0.6002 (mmp)
REVERT: N  104 THR cc_start: 0.8353 (p) cc_final: 0.8118 (t)
REVERT: S   67 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6819 (ttp-110)
REVERT: S  158 SER cc_start: 0.7585 (p) cc_final: 0.7086 (m)
  outliers start: 41
  outliers final: 21
  residues processed: 232
  average time/residue: 0.4899
  time to fit residues: 122.5050
Evaluate side-chains
  238 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  128 MET
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 120 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0570
   chunk 95 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 219 GLN
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
A 278 ASN
B  75 GLN
** B 225 HIS ** 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 = 0.4292 r_free = 0.4292 target = 0.155532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.135587 restraints weight = 15911.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.4023 rms_B_bonded: 2.59
r_work: 0.3904 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9612  Z= 0.161
  Angle     :  0.667   8.382  13043  Z= 0.348
  Chirality :  0.045   0.156   1485
  Planarity :  0.004   0.040   1665
  Dihedral  :  5.084  30.374   1332
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 22.20 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.24), residues: 1207
  helix:  0.77 (0.27), residues: 377
  sheet: -0.98 (0.29), residues: 307
  loop : -1.54 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 129 
 TYR   0.013   0.001   TYR A 318 
 PHE   0.020   0.002   PHE A 222 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.009   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9607)
  covalent geometry    : angle       0.66618 (13033)
  SS BOND              : bond        0.00469 (    5)
  SS BOND              : angle       1.17872 (   10)
  hydrogen bonds       : bond        0.03823 (  422)
  hydrogen bonds       : angle       5.35004 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   25 MET cc_start: 0.6874 (mpp) cc_final: 0.6405 (mpp)
REVERT: A   28 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7489 (mtmm)
REVERT: A   58 LYS cc_start: 0.7669 (tppt) cc_final: 0.7459 (tppt)
REVERT: A  216 LYS cc_start: 0.7624 (mppt) cc_final: 0.7245 (mppt)
REVERT: A  230 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7473 (tt0)
REVERT: A  284 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8033 (p)
REVERT: A  285 ILE cc_start: 0.8882 (mm) cc_final: 0.8556 (tp)
REVERT: A  344 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6448 (mm-30)
REVERT: A  347 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7239 (mtm-85)
REVERT: A  391 TYR cc_start: 0.7696 (m-10) cc_final: 0.6839 (m-10)
REVERT: A  392 GLU cc_start: 0.7661 (mp0) cc_final: 0.7191 (mp0)
REVERT: B    8 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6792 (mtt90)
REVERT: B  100 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8442 (m)
REVERT: G   17 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: G   21 MET cc_start: 0.7648 (ttp) cc_final: 0.7218 (ppp)
REVERT: G   22 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7338 (mt-10)
REVERT: N   34 MET cc_start: 0.6864 (mmt) cc_final: 0.6374 (mmp)
REVERT: N   51 ILE cc_start: 0.7979 (tt) cc_final: 0.7497 (pt)
REVERT: N   83 MET cc_start: 0.6110 (mmp) cc_final: 0.5905 (mmp)
REVERT: S   67 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6873 (ttp-110)
REVERT: S  166 LEU cc_start: 0.7542 (tt) cc_final: 0.7321 (tm)
  outliers start: 38
  outliers final: 20
  residues processed: 227
  average time/residue: 0.4839
  time to fit residues: 118.4127
Evaluate side-chains
  232 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 208
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 CYS
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.155786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.135495 restraints weight = 15803.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 2.61
r_work: 0.3903 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9612  Z= 0.165
  Angle     :  0.681   8.560  13043  Z= 0.356
  Chirality :  0.044   0.158   1485
  Planarity :  0.004   0.040   1665
  Dihedral  :  5.047  29.839   1332
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 22.70 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.24), residues: 1207
  helix:  0.90 (0.27), residues: 377
  sheet: -1.00 (0.29), residues: 306
  loop : -1.49 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG S 160 
 TYR   0.011   0.001   TYR R  74 
 PHE   0.024   0.002   PHE A 222 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.010   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9607)
  covalent geometry    : angle       0.68052 (13033)
  SS BOND              : bond        0.00244 (    5)
  SS BOND              : angle       0.79523 (   10)
  hydrogen bonds       : bond        0.03788 (  422)
  hydrogen bonds       : angle       5.29410 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 209
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  287 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6555 (mt)
REVERT: A   25 MET cc_start: 0.6875 (mpp) cc_final: 0.6405 (mpp)
REVERT: A   28 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7496 (mtmm)
REVERT: A   58 LYS cc_start: 0.7659 (tppt) cc_final: 0.7283 (tmmt)
REVERT: A  216 LYS cc_start: 0.7636 (mppt) cc_final: 0.7244 (mppt)
REVERT: A  230 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7447 (tt0)
REVERT: A  284 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8061 (p)
REVERT: A  340 PHE cc_start: 0.6650 (t80) cc_final: 0.6091 (t80)
REVERT: A  344 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6467 (mm-30)
REVERT: A  391 TYR cc_start: 0.7661 (m-10) cc_final: 0.6736 (m-10)
REVERT: A  392 GLU cc_start: 0.7663 (mp0) cc_final: 0.7144 (mp0)
REVERT: B   61 MET cc_start: 0.7029 (ppp) cc_final: 0.6680 (ppp)
REVERT: B  100 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8402 (m)
REVERT: B  217 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7001 (pp-130)
REVERT: B  336 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7897 (mt)
REVERT: G   17 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7687 (mm-30)
REVERT: G   21 MET cc_start: 0.7686 (ttp) cc_final: 0.7234 (ppp)
REVERT: G   22 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7333 (mt-10)
REVERT: N   34 MET cc_start: 0.6890 (mmt) cc_final: 0.6406 (mmp)
REVERT: N   51 ILE cc_start: 0.7983 (tt) cc_final: 0.7485 (pt)
REVERT: S  166 LEU cc_start: 0.7523 (tt) cc_final: 0.7307 (tm)
  outliers start: 43
  outliers final: 25
  residues processed: 226
  average time/residue: 0.4980
  time to fit residues: 121.0219
Evaluate side-chains
  233 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 CYS
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 120 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 103 optimal weight:    0.0980
   chunk 113 optimal weight:    0.7980
   chunk 109 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9990
   chunk 96 optimal weight:    0.1980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.155208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.134495 restraints weight = 15933.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 2.66
r_work: 0.3910 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9612  Z= 0.150
  Angle     :  0.694   9.004  13043  Z= 0.358
  Chirality :  0.044   0.176   1485
  Planarity :  0.004   0.042   1665
  Dihedral  :  4.987  29.541   1332
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.20 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.87 (0.24), residues: 1207
  helix:  0.99 (0.27), residues: 375
  sheet: -0.95 (0.29), residues: 313
  loop : -1.46 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG S 160 
 TYR   0.015   0.001   TYR A 318 
 PHE   0.029   0.002   PHE A 222 
 TRP   0.057   0.003   TRP B  82 
 HIS   0.009   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9607)
  covalent geometry    : angle       0.69438 (13033)
  SS BOND              : bond        0.00287 (    5)
  SS BOND              : angle       0.71117 (   10)
  hydrogen bonds       : bond        0.03683 (  422)
  hydrogen bonds       : angle       5.28849 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 205
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  287 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6532 (mt)
REVERT: A   25 MET cc_start: 0.6792 (mpp) cc_final: 0.6333 (mpp)
REVERT: A   28 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7472 (mtmm)
REVERT: A   58 LYS cc_start: 0.7655 (tppt) cc_final: 0.7250 (tppt)
REVERT: A  216 LYS cc_start: 0.7629 (mppt) cc_final: 0.7249 (mppt)
REVERT: A  230 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7408 (tt0)
REVERT: A  284 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8056 (p)
REVERT: A  333 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7536 (mtp180)
REVERT: A  340 PHE cc_start: 0.6563 (t80) cc_final: 0.6170 (t80)
REVERT: A  344 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6763 (mm-30)
REVERT: A  347 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7670 (mtm-85)
REVERT: A  391 TYR cc_start: 0.7657 (m-10) cc_final: 0.7024 (m-10)
REVERT: B   61 MET cc_start: 0.7056 (ppp) cc_final: 0.6680 (ppp)
REVERT: B  100 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8287 (m)
REVERT: B  269 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8359 (OUTLIER)
REVERT: G   17 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7689 (mm-30)
REVERT: G   21 MET cc_start: 0.7646 (ttp) cc_final: 0.7188 (ppp)
REVERT: G   22 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7332 (mt-10)
REVERT: N   34 MET cc_start: 0.6884 (mmt) cc_final: 0.6484 (mmp)
REVERT: N   51 ILE cc_start: 0.7965 (tt) cc_final: 0.7489 (pt)
  outliers start: 37
  outliers final: 23
  residues processed: 222
  average time/residue: 0.4879
  time to fit residues: 116.8037
Evaluate side-chains
  229 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 202
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 CYS
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  270 HIS
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 72 optimal weight:    0.3980
   chunk 99 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 ASN
B  75 GLN
B 175 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.151164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.130573 restraints weight = 15852.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 2.63
r_work: 0.3877 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9612  Z= 0.168
  Angle     :  0.717  10.089  13043  Z= 0.370
  Chirality :  0.045   0.179   1485
  Planarity :  0.004   0.040   1665
  Dihedral  :  5.050  29.184   1332
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 25.00 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.84 (0.24), residues: 1207
  helix:  0.93 (0.27), residues: 376
  sheet: -0.95 (0.29), residues: 313
  loop : -1.36 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 333 
 TYR   0.017   0.002   TYR B  85 
 PHE   0.029   0.002   PHE A 222 
 TRP   0.049   0.003   TRP B  82 
 HIS   0.010   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9607)
  covalent geometry    : angle       0.71690 (13033)
  SS BOND              : bond        0.00269 (    5)
  SS BOND              : angle       0.75090 (   10)
  hydrogen bonds       : bond        0.03733 (  422)
  hydrogen bonds       : angle       5.27854 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: R  287 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6604 (mt)
REVERT: A   25 MET cc_start: 0.6790 (mpp) cc_final: 0.6325 (mpp)
REVERT: A   28 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7478 (mtmm)
REVERT: A   58 LYS cc_start: 0.7655 (tppt) cc_final: 0.7342 (tmmt)
REVERT: A  216 LYS cc_start: 0.7623 (mppt) cc_final: 0.7244 (mppt)
REVERT: A  284 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8036 (p)
REVERT: A  344 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6739 (mm-30)
REVERT: A  347 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7683 (mtm-85)
REVERT: A  391 TYR cc_start: 0.7754 (m-10) cc_final: 0.6975 (m-10)
REVERT: A  392 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7066 (mp0)
REVERT: B    8 ARG cc_start: 0.7175 (mtm110) cc_final: 0.6866 (mtt90)
REVERT: B  100 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8306 (m)
REVERT: G   17 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7677 (mm-30)
REVERT: G   22 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7499 (mt-10)
REVERT: N   34 MET cc_start: 0.6887 (mmt) cc_final: 0.6469 (mmp)
REVERT: N   51 ILE cc_start: 0.7963 (tt) cc_final: 0.7495 (pt)
REVERT: N  104 THR cc_start: 0.8415 (p) cc_final: 0.8150 (t)
  outliers start: 35
  outliers final: 22
  residues processed: 219
  average time/residue: 0.4451
  time to fit residues: 105.2111
Evaluate side-chains
  225 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  128 MET
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 CYS
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  270 HIS
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 36 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 118 ASN
** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.152853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.132130 restraints weight = 15786.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 2.65
r_work: 0.3866 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9612  Z= 0.170
  Angle     :  0.723  10.163  13043  Z= 0.372
  Chirality :  0.045   0.188   1485
  Planarity :  0.004   0.044   1665
  Dihedral  :  5.082  29.028   1332
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.20 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.85 (0.24), residues: 1207
  helix:  0.90 (0.27), residues: 382
  sheet: -0.90 (0.29), residues: 313
  loop : -1.42 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 333 
 TYR   0.022   0.002   TYR A 318 
 PHE   0.030   0.002   PHE A 222 
 TRP   0.043   0.003   TRP B  82 
 HIS   0.009   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9607)
  covalent geometry    : angle       0.72287 (13033)
  SS BOND              : bond        0.00272 (    5)
  SS BOND              : angle       0.76835 (   10)
  hydrogen bonds       : bond        0.03764 (  422)
  hydrogen bonds       : angle       5.31343 ( 1215)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 210
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  287 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6588 (mt)
REVERT: A   25 MET cc_start: 0.6793 (mpp) cc_final: 0.6325 (mpp)
REVERT: A   28 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7482 (mtmm)
REVERT: A   58 LYS cc_start: 0.7627 (tppt) cc_final: 0.7231 (tppt)
REVERT: A  216 LYS cc_start: 0.7608 (mppt) cc_final: 0.7188 (mppt)
REVERT: A  284 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8030 (p)
REVERT: A  347 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7631 (mtm-85)
REVERT: A  391 TYR cc_start: 0.7737 (m-10) cc_final: 0.7063 (m-10)
REVERT: A  392 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6965 (mp0)
REVERT: B    8 ARG cc_start: 0.7164 (mtm110) cc_final: 0.6841 (mtt90)
REVERT: B   75 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7666 (mm-40)
REVERT: B  100 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8152 (m)
REVERT: G   17 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7735 (mm-30)
REVERT: G   21 MET cc_start: 0.7565 (ttp) cc_final: 0.7131 (ppp)
REVERT: G   22 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7339 (mt-10)
REVERT: N   34 MET cc_start: 0.6885 (mmt) cc_final: 0.6484 (mmp)
REVERT: N   51 ILE cc_start: 0.7973 (tt) cc_final: 0.7468 (pt)
REVERT: N  104 THR cc_start: 0.8415 (p) cc_final: 0.8157 (t)
REVERT: N  108 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6253 (t80)
  outliers start: 33
  outliers final: 23
  residues processed: 224
  average time/residue: 0.4445
  time to fit residues: 107.7740
Evaluate side-chains
  231 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 202
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 LEU
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  191 CYS
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  203 MET
Chi-restraints excluded: chain R residue  270 HIS
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   chunk 81 optimal weight:   10.0000
   chunk 104 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
B  75 GLN
B 175 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.152437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.131769 restraints weight = 15769.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 2.65
r_work: 0.3877 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.150   9612  Z= 0.247
  Angle     :  0.999  59.197  13043  Z= 0.575
  Chirality :  0.046   0.226   1485
  Planarity :  0.004   0.044   1665
  Dihedral  :  5.101  28.991   1332
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.05 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.00 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.85 (0.24), residues: 1207
  helix:  0.91 (0.27), residues: 382
  sheet: -0.90 (0.29), residues: 313
  loop : -1.43 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 333 
 TYR   0.019   0.002   TYR A 318 
 PHE   0.033   0.003   PHE S 108 
 TRP   0.037   0.003   TRP B  82 
 HIS   0.009   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 9607)
  covalent geometry    : angle       0.99770 (13033)
  SS BOND              : bond        0.00352 (    5)
  SS BOND              : angle       2.27813 (   10)
  hydrogen bonds       : bond        0.03765 (  422)
  hydrogen bonds       : angle       5.32170 ( 1215)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3525.10 seconds
wall clock time: 60 minutes 55.44 seconds (3655.44 seconds total)