Starting phenix.real_space_refine
on Thu Mar 14 20:38:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/03_2024/8iw9_35764_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/03_2024/8iw9_35764.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/03_2024/8iw9_35764.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/03_2024/8iw9_35764.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/03_2024/8iw9_35764_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/03_2024/8iw9_35764_neut.pdb"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      58      5.16       5
     C    6192      2.51       5
     N    1663      2.21       5
     O    1780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   27": "OE1" <-> "OE2"
    Residue "A TYR  358": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  392": "OE1" <-> "OE2"
    Residue "B GLU  130": "OE1" <-> "OE2"
    Residue "B PHE  241": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   58": "OE1" <-> "OE2"
    Residue "R GLU  253": "OE1" <-> "OE2"
    Residue "R ARG  254": "NH1" <-> "NH2"
    Residue "R TYR  302": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S GLU  220": "OE1" <-> "OE2"
    Residue "S GLU  234": "OE1" <-> "OE2"
    Residue "S GLU  246": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9693
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1843
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 66
    Chain: "B"
      Number of atoms: 2488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2488
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 113
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 90
    Chain: "C"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 363
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 43
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2328
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 12, 'TRANS': 296}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 164
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 60
    Chain: "S"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1741
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "N"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 930
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 25
  Time building chain proxies: 5.58, per 1000 atoms: 0.58
  Number of scatterers: 9693
  At special positions: 0
  Unit cell: (106.92, 110.16, 132.84, 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      58     16.00
     O    1780      8.00
     N    1663      7.00
     C    6192      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  22 " - pdb=" SG  CYS R 186 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 125 " - pdb=" SG  CYS R 152 " distance=2.05
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 3.42
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2412

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 16 sheets defined
      33.9% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 39
      removed outlier: 3.869A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.521A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
      removed outlier: 3.506A  pdb=" N   LEU A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.674A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.969A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 4.155A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.523A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 12 through 24
      removed outlier: 4.118A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.594A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'R' and resid 33 through 61
      removed outlier: 3.520A  pdb=" N   ALA R  43 " --> pdb=" O   LEU R  39 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   LYS R  61 " --> pdb=" O   ILE R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 96
      removed outlier: 3.858A  pdb=" N   VAL R  71 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR R  84 " --> pdb=" O   LEU R  80 " (cutoff:3.500A)
      Proline residue:  R  87  - end of helix
    Processing helix  chain 'R' and resid 102 through 136
      removed outlier: 4.424A  pdb=" N   LYS R 106 " --> pdb=" O   GLU R 102 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   PHE R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   CYS R 116 " --> pdb=" O   ASP R 112 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   PHE R 117 " --> pdb=" O   THR R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 168
      removed outlier: 3.611A  pdb=" N   CYS R 152 " --> pdb=" O   VAL R 148 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE R 153 " --> pdb=" O   SER R 149 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TRP R 157 " --> pdb=" O   ILE R 153 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE R 158 " --> pdb=" O   ALA R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 175
      removed outlier: 3.682A  pdb=" N   GLU R 174 " --> pdb=" O   GLY R 171 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLU R 175 " --> pdb=" O   ALA R 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 171 through 175'
    Processing helix  chain 'R' and resid 198 through 232
      Proline residue:  R 209  - end of helix
    Processing helix  chain 'R' and resid 247 through 284
      removed outlier: 3.960A  pdb=" N   LYS R 251 " --> pdb=" O   GLU R 247 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   ARG R 252 " --> pdb=" O   ARG R 248 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS R 255 " --> pdb=" O   LYS R 251 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA R 256 " --> pdb=" O   ARG R 252 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE R 267 " --> pdb=" O   ALA R 263 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 289 through 312
      removed outlier: 3.675A  pdb=" N   TYR R 293 " --> pdb=" O   PRO R 289 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU R 294 " --> pdb=" O   ALA R 290 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE R 295 " --> pdb=" O   TYR R 291 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
      Proline residue:  R 308  - end of helix
    Processing helix  chain 'R' and resid 315 through 328
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.217A  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 62 through 65
      removed outlier: 3.830A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 4.007A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.541A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.988A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.554A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.620A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.911A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.892A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.692A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.991A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.661A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.086A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.513A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.907A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.907A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 4.316A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 5
    Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12
    Processing sheet with id=AB7, first strand: chain 'N' and resid 58 through 60
      removed outlier: 5.353A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)

    451 hydrogen bonds defined for protein.
    1272 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.69

  Time building geometry restraints manager: 3.75 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: 3126
        1.34 -     1.46: 2490
        1.46 -     1.58: 4219
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 9915
  Sorted by residual:
  bond pdb=" CA  ASP B 186 "
       pdb=" C   ASP B 186 "
    ideal  model  delta    sigma   weight residual
    1.524  1.504  0.020 1.30e-02 5.92e+03 2.27e+00
  bond pdb=" CB  GLU R 247 "
       pdb=" CG  GLU R 247 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.17e+00
  bond pdb=" CA  LEU C  37 "
       pdb=" C   LEU C  37 "
    ideal  model  delta    sigma   weight residual
    1.524  1.507  0.017 1.24e-02 6.50e+03 1.92e+00
  bond pdb=" N   LEU R 184 "
       pdb=" CA  LEU R 184 "
    ideal  model  delta    sigma   weight residual
    1.458  1.481 -0.022 1.77e-02 3.19e+03 1.60e+00
  bond pdb=" N   GLU A 309 "
       pdb=" CA  GLU A 309 "
    ideal  model  delta    sigma   weight residual
    1.459  1.475 -0.016 1.28e-02 6.10e+03 1.57e+00
  ... (remaining 9910 not shown)

  Histogram of bond angle deviations from ideal:
      100.25 -   106.99: 237
      106.99 -   113.74: 5418
      113.74 -   120.48: 3720
      120.48 -   127.22: 4019
      127.22 -   133.97: 108
  Bond angle restraints: 13502
  Sorted by residual:
  angle pdb=" N   VAL R 187 "
        pdb=" CA  VAL R 187 "
        pdb=" C   VAL R 187 "
      ideal   model   delta    sigma   weight residual
     110.62  116.80   -6.18 1.02e+00 9.61e-01 3.67e+01
  angle pdb=" N   THR B 165 "
        pdb=" CA  THR B 165 "
        pdb=" C   THR B 165 "
      ideal   model   delta    sigma   weight residual
     110.50  118.48   -7.98 1.41e+00 5.03e-01 3.21e+01
  angle pdb=" N   CYS B 233 "
        pdb=" CA  CYS B 233 "
        pdb=" C   CYS B 233 "
      ideal   model   delta    sigma   weight residual
     112.59  119.46   -6.87 1.22e+00 6.72e-01 3.18e+01
  angle pdb=" N   ASN A 218 "
        pdb=" CA  ASN A 218 "
        pdb=" C   ASN A 218 "
      ideal   model   delta    sigma   weight residual
     109.95  117.74   -7.79 1.59e+00 3.96e-01 2.40e+01
  angle pdb=" N   THR R  67 "
        pdb=" CA  THR R  67 "
        pdb=" C   THR R  67 "
      ideal   model   delta    sigma   weight residual
     113.41  107.75    5.66 1.22e+00 6.72e-01 2.15e+01
  ... (remaining 13497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 5151
       17.12 -    34.25: 466
       34.25 -    51.37: 143
       51.37 -    68.49: 17
       68.49 -    85.62: 9
  Dihedral angle restraints: 5786
    sinusoidal: 2037
      harmonic: 3749
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.19  -80.81     1      1.00e+01 1.00e-02 8.07e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.07   34.93     1      1.00e+01 1.00e-02 1.73e+01
  dihedral pdb=" CB  CYS R  22 "
           pdb=" SG  CYS R  22 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.23   34.23     1      1.00e+01 1.00e-02 1.66e+01
  ... (remaining 5783 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1377
       0.071 -    0.142: 158
       0.142 -    0.213: 10
       0.213 -    0.284: 2
       0.284 -    0.354: 1
  Chirality restraints: 1548
  Sorted by residual:
  chirality pdb=" CA  LEU R 184 "
            pdb=" N   LEU R 184 "
            pdb=" C   LEU R 184 "
            pdb=" CB  LEU R 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.14e+00
  chirality pdb=" CA  CYS B 233 "
            pdb=" N   CYS B 233 "
            pdb=" C   CYS B 233 "
            pdb=" CB  CYS B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  ARG R 332 "
            pdb=" N   ARG R 332 "
            pdb=" C   ARG R 332 "
            pdb=" CB  ARG R 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1545 not shown)

  Planarity restraints: 1717
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 217 "    0.012 2.00e-02 2.50e+03   2.42e-02 5.84e+00
        pdb=" C   VAL A 217 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   VAL A 217 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASN A 218 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 162 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.22e+00
        pdb=" C   GLY B 162 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLY B 162 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ASP B 163 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  81 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.13e+00
        pdb=" C   VAL R  81 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   VAL R  81 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY R  82 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1714 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 339
        2.71 -     3.26: 9499
        3.26 -     3.81: 15014
        3.81 -     4.35: 17960
        4.35 -     4.90: 32261
  Nonbonded interactions: 75073
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.168 2.440
  nonbonded pdb=" O   SER R  26 "
            pdb=" OG  SER R  96 "
     model   vdw
     2.169 2.440
  nonbonded pdb=" N   GLU C  58 "
            pdb=" OE1 GLU C  58 "
     model   vdw
     2.205 2.520
  nonbonded pdb=" OD2 ASP R 112 "
            pdb=" OH  TYR R 301 "
     model   vdw
     2.219 2.440
  nonbonded pdb=" N   GLU B 130 "
            pdb=" OE1 GLU B 130 "
     model   vdw
     2.249 2.520
  ... (remaining 75068 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.330
  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:          2.290
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     27.780
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
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      :  0.003   0.044   9915  Z= 0.218
  Angle     :  0.663   7.984  13502  Z= 0.407
  Chirality :  0.046   0.354   1548
  Planarity :  0.004   0.042   1717
  Dihedral  : 14.652  85.618   3359
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 17.73 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.24), residues: 1273
  helix:  1.52 (0.28), residues: 388
  sheet:  0.47 (0.29), residues: 317
  loop : -1.03 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.009   0.001   PHE R  60 
 TYR   0.026   0.001   TYR S 235 
 ARG   0.012   0.000   ARG A 356 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  229 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7895 (tpp80)
REVERT: N   77 ASN cc_start: 0.9105 (m-40) cc_final: 0.8871 (m-40)
  outliers start: 6
  outliers final: 6
  residues processed: 127
  average time/residue: 0.2437
  time to fit residues: 43.2354
Evaluate side-chains
  119 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  326 VAL
Chi-restraints excluded: chain S residue   48 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.1980
   chunk 95 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0970
   chunk 73 optimal weight:    2.9990
   chunk 114 optimal weight:   10.0000
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 119 ASN
C  11 GLN
R 196 GLN
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9915  Z= 0.155
  Angle     :  0.516   5.584  13502  Z= 0.278
  Chirality :  0.041   0.187   1548
  Planarity :  0.003   0.035   1717
  Dihedral  :  4.265  40.982   1406
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.68 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.24), residues: 1273
  helix:  2.39 (0.27), residues: 388
  sheet:  0.71 (0.30), residues: 307
  loop : -0.92 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R  60 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.008   0.000   ARG S  87 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
REVERT: B   46 ARG cc_start: 0.8766 (ptp-170) cc_final: 0.8557 (ptp90)
REVERT: S   76 LYS cc_start: 0.9411 (mtpp) cc_final: 0.9176 (mtmm)
  outliers start: 20
  outliers final: 11
  residues processed: 146
  average time/residue: 0.2269
  time to fit residues: 45.7881
Evaluate side-chains
  125 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  258 LYS
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0570
   chunk 77 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 114 optimal weight:    9.9990
   chunk 123 optimal weight:    8.9990
   chunk 102 optimal weight:   10.0000
   chunk 113 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    3.0106

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 220 GLN
C  11 GLN
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9915  Z= 0.316
  Angle     :  0.565   7.305  13502  Z= 0.305
  Chirality :  0.043   0.243   1548
  Planarity :  0.004   0.040   1717
  Dihedral  :  4.439  40.380   1403
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.68 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.24), residues: 1273
  helix:  2.49 (0.27), residues: 396
  sheet:  0.76 (0.30), residues: 301
  loop : -1.01 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.023   0.001   PHE R  60 
 TYR   0.033   0.001   TYR S 235 
 ARG   0.004   0.000   ARG R 252 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8222 (mm110)
REVERT: R   78 ASP cc_start: 0.7465 (t70) cc_final: 0.7153 (t70)
REVERT: R  229 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8026 (tpp80)
REVERT: S   76 LYS cc_start: 0.9454 (mtpp) cc_final: 0.9241 (mtmm)
REVERT: S  246 GLU cc_start: 0.7178 (pm20) cc_final: 0.6803 (pm20)
  outliers start: 29
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2249
  time to fit residues: 42.3460
Evaluate side-chains
  127 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  204 LEU
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  277 ASP
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 109 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
C  11 GLN
** R  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054   9915  Z= 0.503
  Angle     :  0.639   8.704  13502  Z= 0.347
  Chirality :  0.046   0.276   1548
  Planarity :  0.004   0.044   1717
  Dihedral  :  4.811  40.251   1403
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.98 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1273
  helix:  2.19 (0.26), residues: 399
  sheet:  0.35 (0.29), residues: 323
  loop : -1.09 (0.25), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.025   0.002   PHE R  60 
 TYR   0.039   0.002   TYR S 235 
 ARG   0.004   0.000   ARG S  87 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 110
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8235 (mm110)
REVERT: B   59 TYR cc_start: 0.9481 (OUTLIER) cc_final: 0.8828 (m-80)
REVERT: R   78 ASP cc_start: 0.7531 (t70) cc_final: 0.7251 (t70)
REVERT: R  136 ASP cc_start: 0.8802 (t70) cc_final: 0.8582 (t70)
REVERT: S   81 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8564 (pt)
REVERT: S  246 GLU cc_start: 0.7430 (pm20) cc_final: 0.7178 (pm20)
  outliers start: 39
  outliers final: 25
  residues processed: 138
  average time/residue: 0.2266
  time to fit residues: 43.9469
Evaluate side-chains
  132 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  204 LEU
Chi-restraints excluded: chain R residue  231 ILE
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  277 ASP
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  220 GLU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 69 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 109 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9915  Z= 0.160
  Angle     :  0.500   6.587  13502  Z= 0.268
  Chirality :  0.041   0.196   1548
  Planarity :  0.003   0.041   1717
  Dihedral  :  4.322  40.727   1402
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.32 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1273
  helix:  2.65 (0.26), residues: 395
  sheet:  0.66 (0.30), residues: 307
  loop : -0.99 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 298 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.022   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 229 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  112 ASP cc_start: 0.8183 (t70) cc_final: 0.7345 (t70)
REVERT: R  225 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8278 (ttmm)
REVERT: S   76 LYS cc_start: 0.9503 (mtpp) cc_final: 0.9289 (mtmm)
REVERT: S   87 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8495 (mtt-85)
REVERT: S  246 GLU cc_start: 0.7427 (pm20) cc_final: 0.7023 (pm20)
REVERT: N  106 ASP cc_start: 0.8031 (p0) cc_final: 0.7719 (p0)
  outliers start: 27
  outliers final: 17
  residues processed: 135
  average time/residue: 0.2244
  time to fit residues: 43.1373
Evaluate side-chains
  123 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  258 LYS
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  220 GLU
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 109 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 117 optimal weight:    8.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  32 GLN
C  11 GLN
R  64 HIS
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   9915  Z= 0.364
  Angle     :  0.576   6.957  13502  Z= 0.311
  Chirality :  0.044   0.234   1548
  Planarity :  0.004   0.041   1717
  Dihedral  :  4.530  40.605   1402
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.91 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.24), residues: 1273
  helix:  2.55 (0.26), residues: 394
  sheet:  0.65 (0.30), residues: 301
  loop : -1.09 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R  60 
 TYR   0.029   0.001   TYR S 235 
 ARG   0.004   0.000   ARG R 229 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 107
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.9489 (OUTLIER) cc_final: 0.8741 (m-80)
REVERT: S   81 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8266 (pt)
REVERT: S   87 ARG cc_start: 0.8758 (mtt-85) cc_final: 0.8543 (mtt-85)
REVERT: S  246 GLU cc_start: 0.7516 (pm20) cc_final: 0.7104 (pm20)
REVERT: N  106 ASP cc_start: 0.8265 (p0) cc_final: 0.8006 (p0)
  outliers start: 35
  outliers final: 23
  residues processed: 133
  average time/residue: 0.2407
  time to fit residues: 44.7547
Evaluate side-chains
  129 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  204 LEU
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  277 ASP
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  220 GLU
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 89 optimal weight:    0.0980
   chunk 68 optimal weight:    7.9990
   chunk 102 optimal weight:    3.9990
   chunk 121 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    3.6188

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  32 GLN
C  11 GLN
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   9915  Z= 0.369
  Angle     :  0.586   7.501  13502  Z= 0.317
  Chirality :  0.044   0.242   1548
  Planarity :  0.004   0.040   1717
  Dihedral  :  4.638  40.954   1402
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.70 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.24), residues: 1273
  helix:  2.51 (0.26), residues: 394
  sheet:  0.52 (0.30), residues: 313
  loop : -1.08 (0.25), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R  60 
 TYR   0.031   0.001   TYR S 235 
 ARG   0.006   0.000   ARG R 252 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 GLU cc_start: 0.8592 (pm20) cc_final: 0.8360 (pm20)
REVERT: B   59 TYR cc_start: 0.9489 (OUTLIER) cc_final: 0.8741 (m-80)
REVERT: S   76 LYS cc_start: 0.9530 (mtmm) cc_final: 0.9218 (mtmm)
REVERT: S   81 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8439 (pt)
REVERT: S   87 ARG cc_start: 0.8767 (mtt-85) cc_final: 0.8549 (mtt-85)
  outliers start: 39
  outliers final: 29
  residues processed: 136
  average time/residue: 0.2073
  time to fit residues: 39.9073
Evaluate side-chains
  136 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  204 LEU
Chi-restraints excluded: chain R residue  267 PHE
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  277 ASP
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  220 GLU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 77 optimal weight:   50.0000
   chunk 82 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 95 optimal weight:    4.9990
   chunk 110 optimal weight:    9.9990
   chunk 116 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  32 GLN
C  11 GLN
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9915  Z= 0.204
  Angle     :  0.523   8.324  13502  Z= 0.279
  Chirality :  0.042   0.199   1548
  Planarity :  0.003   0.039   1717
  Dihedral  :  4.356  41.197   1402
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.42 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1273
  helix:  2.76 (0.26), residues: 395
  sheet:  0.71 (0.30), residues: 305
  loop : -0.99 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.022   0.001   TYR S 235 
 ARG   0.005   0.000   ARG R 252 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 GLU cc_start: 0.8577 (pm20) cc_final: 0.8303 (pm20)
REVERT: B   59 TYR cc_start: 0.9474 (OUTLIER) cc_final: 0.8646 (m-80)
REVERT: R  191 GLN cc_start: 0.8909 (mt0) cc_final: 0.8699 (mt0)
REVERT: S   76 LYS cc_start: 0.9529 (mtmm) cc_final: 0.9267 (mtmm)
REVERT: S   81 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8111 (pt)
  outliers start: 30
  outliers final: 23
  residues processed: 132
  average time/residue: 0.2283
  time to fit residues: 42.5807
Evaluate side-chains
  129 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 2.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  204 LEU
Chi-restraints excluded: chain R residue  258 LYS
Chi-restraints excluded: chain R residue  267 PHE
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  192 MET
Chi-restraints excluded: chain S residue  220 GLU
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    0.6980
   chunk 116 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 102 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
C  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9915  Z= 0.177
  Angle     :  0.514   8.462  13502  Z= 0.274
  Chirality :  0.041   0.188   1548
  Planarity :  0.003   0.042   1717
  Dihedral  :  4.239  40.874   1402
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.83 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.24), residues: 1273
  helix:  2.83 (0.26), residues: 395
  sheet:  0.78 (0.30), residues: 305
  loop : -0.93 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.010   0.001   PHE R  60 
 TYR   0.022   0.001   TYR S 235 
 ARG   0.007   0.000   ARG S  87 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 GLU cc_start: 0.8565 (pm20) cc_final: 0.8254 (pm20)
REVERT: B   59 TYR cc_start: 0.9475 (OUTLIER) cc_final: 0.8644 (m-80)
REVERT: R  191 GLN cc_start: 0.8875 (mt0) cc_final: 0.8669 (mt0)
REVERT: S   76 LYS cc_start: 0.9531 (mtmm) cc_final: 0.9256 (mtmm)
REVERT: S   81 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8120 (pt)
  outliers start: 28
  outliers final: 24
  residues processed: 129
  average time/residue: 0.2176
  time to fit residues: 39.5843
Evaluate side-chains
  134 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  204 LEU
Chi-restraints excluded: chain R residue  258 LYS
Chi-restraints excluded: chain R residue  267 PHE
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  220 GLU
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 73 optimal weight:    0.0980
   chunk 56 optimal weight:    8.9990
   chunk 83 optimal weight:    8.9990
   chunk 125 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:   30.0000
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    0.3980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
C  11 GLN
R  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9915  Z= 0.160
  Angle     :  0.511   8.778  13502  Z= 0.271
  Chirality :  0.041   0.175   1548
  Planarity :  0.003   0.043   1717
  Dihedral  :  4.117  39.920   1402
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.93 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1273
  helix:  2.90 (0.26), residues: 395
  sheet:  0.81 (0.30), residues: 305
  loop : -0.90 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 298 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.019   0.001   TYR S 235 
 ARG   0.007   0.000   ARG S  87 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 GLU cc_start: 0.8585 (pm20) cc_final: 0.8219 (pm20)
REVERT: B   59 TYR cc_start: 0.9467 (OUTLIER) cc_final: 0.8620 (m-80)
REVERT: R  191 GLN cc_start: 0.8831 (mt0) cc_final: 0.8593 (mt0)
REVERT: R  225 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8625 (tttm)
REVERT: S   76 LYS cc_start: 0.9532 (mtmm) cc_final: 0.9259 (mtmm)
REVERT: S   81 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8101 (pt)
REVERT: N   38 ARG cc_start: 0.9128 (ptt180) cc_final: 0.8908 (ptt180)
  outliers start: 29
  outliers final: 24
  residues processed: 135
  average time/residue: 0.2278
  time to fit residues: 43.0535
Evaluate side-chains
  135 residues out of total 1101 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   62 GLN
Chi-restraints excluded: chain R residue   63 LEU
Chi-restraints excluded: chain R residue   99 TYR
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  258 LYS
Chi-restraints excluded: chain R residue  267 PHE
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  220 GLU
Chi-restraints excluded: chain N residue  124 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0000
   overall best weight:    1.9992

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
C  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.078565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.056956 restraints weight = 22330.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 2.69
r_work: 0.2601 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2478 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8731
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.274   9915  Z= 0.257
  Angle     :  0.827  65.899  13502  Z= 0.479
  Chirality :  0.042   0.342   1548
  Planarity :  0.007   0.245   1717
  Dihedral  :  4.127  39.917   1402
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.14 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1273
  helix:  2.89 (0.26), residues: 395
  sheet:  0.82 (0.30), residues: 305
  loop : -0.90 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.019   0.001   TYR S 235 
 ARG   0.006   0.000   ARG S  87 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2165.10 seconds
wall clock time: 39 minutes 37.79 seconds (2377.79 seconds total)