Starting phenix.real_space_refine
on Mon Mar 11 12:05:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/03_2024/7y27_33587_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/03_2024/7y27_33587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/03_2024/7y27_33587.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/03_2024/7y27_33587.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/03_2024/7y27_33587_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y27_33587/03_2024/7y27_33587_updated.pdb"
  }
  resolution = 3.48
  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=  -0.002 sd=   0.130
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      51      5.16       5
     C    5241      2.51       5
     N    1372      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  130": "OE1" <-> "OE2"
    Residue "A PHE  241": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  258": "OD1" <-> "OD2"
    Residue "A ASP  333": "OD1" <-> "OD2"
    Residue "B GLU    8": "OE1" <-> "OE2"
    Residue "B PHE   70": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  111": "OD1" <-> "OD2"
    Residue "B TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  124": "OD1" <-> "OD2"
    Residue "B PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  166": "OE1" <-> "OE2"
    Residue "B ASP  199": "OD1" <-> "OD2"
    Residue "D PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   95": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  251": "OE1" <-> "OE2"
    Residue "C PHE    6": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE    7": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 8184
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2419
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 183
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 130
    Chain: "B"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1724
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 164
          Unresolved non-hydrogen angles: 193
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 8, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 96
    Chain: "D"
      Number of atoms: 1683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1683
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 60
    Chain: "E"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 1901
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 70}
          Link IDs: {'PTRANS': 11, 'TRANS': 262}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 288
          Unresolved non-hydrogen angles: 358
          Unresolved non-hydrogen dihedrals: 257
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 147
    Chain: "F"
      Number of atoms: 327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 327
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 102
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.83, per 1000 atoms: 0.59
  Number of scatterers: 8184
  At special positions: 0
  Unit cell: (93.74, 128.14, 129.86, 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      51     16.00
     O    1520      8.00
     N    1372      7.00
     C    5241      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 115 " - pdb=" SG  CYS E 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   3 " - pdb=" SG  CYS C  14 " 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: 2.96
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      23 helices and 16 sheets defined
      33.6% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 25
    Processing helix  chain 'A' and resid 30 through 36
      removed outlier: 5.117A  pdb=" N   ASN A  36 " --> pdb=" O   GLN A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'B' and resid 7 through 31
      removed outlier: 3.898A  pdb=" N   ALA B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ARG B  31 " --> pdb=" O   GLY B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 94 through 98
    Processing helix  chain 'B' and resid 118 through 130
    Processing helix  chain 'B' and resid 146 through 155
    Processing helix  chain 'B' and resid 160 through 163
      No H-bonds generated for 'chain 'B' and resid 160 through 163'
    Processing helix  chain 'B' and resid 184 through 203
      removed outlier: 4.034A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 242
    Processing helix  chain 'E' and resid 41 through 70
      removed outlier: 3.706A  pdb=" N   VAL E  53 " --> pdb=" O   ILE E  49 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS E  54 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE E  55 " --> pdb=" O   PHE E  51 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE E  56 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 105
      removed outlier: 3.626A  pdb=" N   GLY E  95 " --> pdb=" O   PHE E  92 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LEU E  96 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
      Proline residue:  E  97  - end of helix
      removed outlier: 3.504A  pdb=" N   MET E 101 " --> pdb=" O   PHE E  98 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU E 105 " --> pdb=" O   GLN E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 112 through 145
      removed outlier: 4.488A  pdb=" N   ARG E 116 " --> pdb=" O   LYS E 112 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   VAL E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE E 130 " --> pdb=" O   GLN E 126 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   PHE E 131 " --> pdb=" O   PHE E 127 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 153
    Processing helix  chain 'E' and resid 156 through 179
      removed outlier: 4.149A  pdb=" N   LYS E 160 " --> pdb=" O   PRO E 156 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR E 163 " --> pdb=" O   ALA E 159 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   MET E 164 " --> pdb=" O   LYS E 160 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU E 175 " --> pdb=" O   LEU E 171 " (cutoff:3.500A)
      Proline residue:  E 176  - end of helix
    Processing helix  chain 'E' and resid 203 through 214
    Processing helix  chain 'E' and resid 218 through 237
      removed outlier: 3.643A  pdb=" N   THR E 222 " --> pdb=" O   LEU E 218 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 251 through 281
      removed outlier: 3.528A  pdb=" N   ARG E 256 " --> pdb=" O   LYS E 252 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ALA E 263 " --> pdb=" O   SER E 259 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE E 265 " --> pdb=" O   VAL E 261 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TRP E 269 " --> pdb=" O   PHE E 265 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU E 270 " --> pdb=" O   ILE E 266 " (cutoff:3.500A)
      Proline residue:  E 271  - end of helix
      removed outlier: 3.694A  pdb=" N   VAL E 277 " --> pdb=" O   TYR E 273 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 288 through 313
      removed outlier: 3.561A  pdb=" N   PHE E 296 " --> pdb=" O   GLY E 292 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL E 297 " --> pdb=" O   MET E 293 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL E 298 " --> pdb=" O   PHE E 294 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL E 299 " --> pdb=" O   ASP E 295 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ASN E 304 " --> pdb=" O   LEU E 300 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   SER E 305 " --> pdb=" O   THR E 301 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   CYS E 306 " --> pdb=" O   TYR E 302 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA E 307 " --> pdb=" O   ALA E 303 " (cutoff:3.500A)
      Proline residue:  E 309  - end of helix
      removed outlier: 3.631A  pdb=" N   TYR E 312 " --> pdb=" O   ASN E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 317 through 323
    Processing helix  chain 'F' and resid 12 through 23
    Processing helix  chain 'F' and resid 30 through 43
    Processing sheet with id=  A, first strand: chain 'A' and resid 58 through 63
      removed outlier: 3.563A  pdb=" N   TYR A  59 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ALA A  73 " --> pdb=" O   TYR A  59 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   MET A  61 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   VAL A  71 " --> pdb=" O   MET A  61 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   TRP A  63 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LEU A  69 " --> pdb=" O   TRP A  63 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER A  74 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   LYS A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   HIS A  91 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP A  83 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   LYS A  89 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 103 through 105
      removed outlier: 3.658A  pdb=" N   ARG A 137 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ASN A 125 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   VAL A 135 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 178 through 180
      removed outlier: 3.823A  pdb=" N   THR A 178 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS A 166 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   THR A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ILE A 157 " --> pdb=" O   TRP A 169 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 220 through 222
      removed outlier: 3.601A  pdb=" N   GLN A 220 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   SER A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 203 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A 209 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 200 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLY A 202 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER A 189 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 276 through 278
      removed outlier: 3.558A  pdb=" N   LEU A 308 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 306 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ASP A 298 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG A 304 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'A' and resid 46 through 50
      removed outlier: 3.765A  pdb=" N   ARG A  46 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASN A 340 " --> pdb=" O   ARG A  46 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG A  48 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ILE A 338 " --> pdb=" O   ARG A  48 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS A 317 " --> pdb=" O   GLY A 330 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'A' and resid 229 through 234
      removed outlier: 7.063A  pdb=" N   GLY A 244 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ILE A 232 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'A' and resid 250 through 254
      removed outlier: 3.667A  pdb=" N   LEU A 252 " --> pdb=" O   MET A 262 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   MET A 262 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   ASP A 254 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   GLU A 260 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 138 through 144
      removed outlier: 3.541A  pdb=" N   VAL B 110 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASN B 144 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   ARG B  35 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 9.350A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=  K, first strand: chain 'D' and resid 115 through 117
      removed outlier: 3.963A  pdb=" N   VAL D  97 " --> pdb=" O   HIS D  35 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   HIS D  35 " --> pdb=" O   VAL D  97 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER D  99 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'D' and resid 128 through 130
    Processing sheet with id=  M, first strand: chain 'D' and resid 134 through 136
      removed outlier: 6.242A  pdb=" N   LYS D 232 " --> pdb=" O   VAL D 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  M
    Processing sheet with id=  N, first strand: chain 'D' and resid 214 through 219
      removed outlier: 3.771A  pdb=" N   ILE D 177 " --> pdb=" O   TRP D 164 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LEU D 166 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   LEU D 175 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'E' and resid 184 through 186
    Processing sheet with id=  P, first strand: chain 'C' and resid 5 through 7
      removed outlier: 4.571A  pdb=" N   ASN C   5 " --> pdb=" O   THR C  12 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   THR C  12 " --> pdb=" O   ASN C   5 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE C   7 " --> pdb=" O   THR C  10 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    981 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: 2.30

  Time building geometry restraints manager: 3.18 seconds

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

  Histogram of bond lengths:
        1.05 -     1.20: 3
        1.20 -     1.36: 2665
        1.36 -     1.51: 2456
        1.51 -     1.66: 3163
        1.66 -     1.82: 74
  Bond restraints: 8361
  Sorted by residual:
  bond pdb=" C10 CLR E 401 "
       pdb=" C9  CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.551  1.052  0.499 2.00e-02 2.50e+03 6.24e+02
  bond pdb=" C1  CLR E 401 "
       pdb=" C10 CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.544  1.125  0.419 2.00e-02 2.50e+03 4.39e+02
  bond pdb=" C6  CLR E 401 "
       pdb=" C7  CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.492  1.089  0.403 2.00e-02 2.50e+03 4.05e+02
  bond pdb=" C3  CLR E 401 "
       pdb=" C4  CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.526  1.209  0.317 2.00e-02 2.50e+03 2.50e+02
  bond pdb=" C13 CLR E 401 "
       pdb=" C17 CLR E 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.253  0.297 2.00e-02 2.50e+03 2.21e+02
  ... (remaining 8356 not shown)

  Histogram of bond angle deviations from ideal:
       99.22 -   106.17: 174
      106.17 -   113.12: 4572
      113.12 -   120.07: 2740
      120.07 -   127.02: 3859
      127.02 -   133.97: 95
  Bond angle restraints: 11440
  Sorted by residual:
  angle pdb=" N   ILE A 270 "
        pdb=" CA  ILE A 270 "
        pdb=" C   ILE A 270 "
      ideal   model   delta    sigma   weight residual
     113.71  108.69    5.02 9.50e-01 1.11e+00 2.79e+01
  angle pdb=" C4  CLR E 401 "
        pdb=" C5  CLR E 401 "
        pdb=" C6  CLR E 401 "
      ideal   model   delta    sigma   weight residual
     120.33  108.10   12.23 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C   LEU E 105 "
        pdb=" N   VAL E 106 "
        pdb=" CA  VAL E 106 "
      ideal   model   delta    sigma   weight residual
     121.97  129.29   -7.32 1.80e+00 3.09e-01 1.66e+01
  angle pdb=" CA  GLU A 130 "
        pdb=" CB  GLU A 130 "
        pdb=" CG  GLU A 130 "
      ideal   model   delta    sigma   weight residual
     114.10  121.89   -7.79 2.00e+00 2.50e-01 1.52e+01
  angle pdb=" CA  PRO B 165 "
        pdb=" N   PRO B 165 "
        pdb=" CD  PRO B 165 "
      ideal   model   delta    sigma   weight residual
     112.00  106.75    5.25 1.40e+00 5.10e-01 1.40e+01
  ... (remaining 11435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.35: 4560
       19.35 -    38.70: 276
       38.70 -    58.06: 45
       58.06 -    77.41: 9
       77.41 -    96.76: 6
  Dihedral angle restraints: 4896
    sinusoidal: 1603
      harmonic: 3293
  Sorted by residual:
  dihedral pdb=" CB  CYS C   3 "
           pdb=" SG  CYS C   3 "
           pdb=" SG  CYS C  14 "
           pdb=" CB  CYS C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    2.41  -88.41     1      1.00e+01 1.00e-02 9.33e+01
  dihedral pdb=" CB  CYS D 147 "
           pdb=" SG  CYS D 147 "
           pdb=" SG  CYS D 217 "
           pdb=" CB  CYS D 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.90  -37.90     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CA  PHE E 217 "
           pdb=" C   PHE E 217 "
           pdb=" N   LEU E 218 "
           pdb=" CA  LEU E 218 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.334: 1364
       0.334 -    0.668: 2
       0.668 -    1.001: 0
       1.001 -    1.335: 0
       1.335 -    1.669: 1
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" C10 CLR E 401 "
            pdb=" C1  CLR E 401 "
            pdb=" C5  CLR E 401 "
            pdb=" C9  CLR E 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -1.18   -1.67 2.00e-01 2.50e+01 6.96e+01
  chirality pdb=" C9  CLR E 401 "
            pdb=" C10 CLR E 401 "
            pdb=" C11 CLR E 401 "
            pdb=" C8  CLR E 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.10   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" C3  CLR E 401 "
            pdb=" C2  CLR E 401 "
            pdb=" C4  CLR E 401 "
            pdb=" O1  CLR E 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46   -2.12   -0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 1364 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 175 "   -0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO E 176 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO E 176 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO E 176 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 244 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.17e+00
        pdb=" C   ASN B 244 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ASN B 244 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU B 245 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 219 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.44e+00
        pdb=" N   PRO E 220 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO E 220 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E 220 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 677
        2.74 -     3.28: 7895
        3.28 -     3.82: 12253
        3.82 -     4.36: 12752
        4.36 -     4.90: 24093
  Nonbonded interactions: 57670
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 163 "
            pdb=" OG1 THR A 165 "
     model   vdw
     2.204 2.440
  nonbonded pdb=" O   ASN B 244 "
            pdb=" ND2 ASN B 244 "
     model   vdw
     2.229 2.520
  nonbonded pdb=" ND2 ASN A 230 "
            pdb=" OD1 ASP A 246 "
     model   vdw
     2.257 2.520
  nonbonded pdb=" O   PHE E 275 "
            pdb=" OG  SER E 278 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" OD1 ASP A 247 "
            pdb=" OG1 THR A 249 "
     model   vdw
     2.266 2.440
  ... (remaining 57665 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:             1.200
  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:          3.410
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     25.480
  Find NCS groups from input model:        0.240
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
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      :  0.012   0.499   8361  Z= 0.925
  Angle     :  0.625  12.233  11440  Z= 0.332
  Chirality :  0.062   1.669   1367
  Planarity :  0.004   0.057   1450
  Dihedral  : 13.374  96.759   2759
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.16 (0.25), residues: 1115
  helix:  2.02 (0.28), residues: 358
  sheet:  0.09 (0.31), residues: 284
  loop : -1.42 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 269 
 HIS   0.003   0.001   HIS F  44 
 PHE   0.011   0.001   PHE B  70 
 TYR   0.013   0.001   TYR E 180 
 ARG   0.005   0.000   ARG D 168 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 GLN cc_start: 0.8124 (pt0) cc_final: 0.7886 (pt0)
REVERT: B  167 PHE cc_start: 0.7579 (t80) cc_final: 0.7187 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1881
  time to fit residues: 41.8971
Evaluate side-chains
  127 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 146 GLN
B 244 ASN
D 171 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8361  Z= 0.232
  Angle     :  0.560   6.962  11440  Z= 0.300
  Chirality :  0.041   0.141   1367
  Planarity :  0.004   0.047   1450
  Dihedral  :  4.630  41.576   1267
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.04 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  8.54 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.27 (0.26), residues: 1115
  helix:  2.39 (0.28), residues: 358
  sheet: -0.01 (0.31), residues: 288
  loop : -1.51 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 129 
 HIS   0.004   0.001   HIS D  35 
 PHE   0.010   0.001   PHE E 217 
 TYR   0.014   0.001   TYR F  40 
 ARG   0.003   0.000   ARG D  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8156 (pt0) cc_final: 0.7946 (pt0)
REVERT: B   43 ASN cc_start: 0.7431 (t0) cc_final: 0.7095 (t0)
REVERT: B  167 PHE cc_start: 0.7609 (t80) cc_final: 0.7291 (t80)
REVERT: D  159 ASN cc_start: 0.8951 (m110) cc_final: 0.8591 (m110)
  outliers start: 12
  outliers final: 10
  residues processed: 151
  average time/residue: 0.1611
  time to fit residues: 35.1444
Evaluate side-chains
  152 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 CYS
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  278 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 69 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 110 optimal weight:    0.3980
   chunk 90 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8361  Z= 0.140
  Angle     :  0.488   6.660  11440  Z= 0.260
  Chirality :  0.039   0.133   1367
  Planarity :  0.004   0.043   1450
  Dihedral  :  4.106  32.350   1267
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.50 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.77 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.39 (0.26), residues: 1115
  helix:  2.50 (0.28), residues: 359
  sheet:  0.02 (0.31), residues: 293
  loop : -1.44 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 129 
 HIS   0.003   0.001   HIS E 107 
 PHE   0.010   0.001   PHE B  74 
 TYR   0.010   0.001   TYR B 115 
 ARG   0.003   0.000   ARG D 168 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A   57 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7500 (mttp)
REVERT: A  228 ASP cc_start: 0.7651 (m-30) cc_final: 0.7135 (m-30)
REVERT: A  254 ASP cc_start: 0.8574 (t0) cc_final: 0.7884 (m-30)
REVERT: A  259 GLN cc_start: 0.8096 (pt0) cc_final: 0.7863 (pt0)
REVERT: B   43 ASN cc_start: 0.7426 (t0) cc_final: 0.7099 (t0)
REVERT: B  111 ASP cc_start: 0.8430 (t0) cc_final: 0.8082 (t0)
REVERT: B  146 GLN cc_start: 0.7648 (mt0) cc_final: 0.7425 (mt0)
REVERT: B  167 PHE cc_start: 0.7654 (t80) cc_final: 0.7340 (t80)
REVERT: D  159 ASN cc_start: 0.8930 (m110) cc_final: 0.8581 (m110)
  outliers start: 16
  outliers final: 10
  residues processed: 163
  average time/residue: 0.1812
  time to fit residues: 43.2119
Evaluate side-chains
  158 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 52 optimal weight:    8.9990
   chunk 11 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0870
   chunk 102 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0470
   overall best weight:    1.1460

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8361  Z= 0.164
  Angle     :  0.511   7.937  11440  Z= 0.270
  Chirality :  0.040   0.213   1367
  Planarity :  0.004   0.041   1450
  Dihedral  :  4.021  30.883   1267
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.59 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.68 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.40 (0.26), residues: 1115
  helix:  2.50 (0.28), residues: 359
  sheet:  0.02 (0.31), residues: 290
  loop : -1.41 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 129 
 HIS   0.003   0.001   HIS E 107 
 PHE   0.010   0.001   PHE B  74 
 TYR   0.011   0.001   TYR B 115 
 ARG   0.003   0.000   ARG D  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A   57 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7341 (mttp)
REVERT: A  151 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8098 (m-80)
REVERT: A  228 ASP cc_start: 0.7701 (m-30) cc_final: 0.7198 (m-30)
REVERT: A  254 ASP cc_start: 0.8563 (t0) cc_final: 0.7813 (m-30)
REVERT: A  259 GLN cc_start: 0.8143 (pt0) cc_final: 0.7925 (pt0)
REVERT: B   43 ASN cc_start: 0.7476 (t0) cc_final: 0.7131 (t0)
REVERT: B  111 ASP cc_start: 0.8480 (t0) cc_final: 0.8121 (t0)
REVERT: B  167 PHE cc_start: 0.7679 (t80) cc_final: 0.7330 (t80)
REVERT: D  159 ASN cc_start: 0.8941 (m110) cc_final: 0.8628 (m110)
  outliers start: 21
  outliers final: 14
  residues processed: 162
  average time/residue: 0.1666
  time to fit residues: 38.6253
Evaluate side-chains
  165 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 1 optimal weight:   50.0000
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 92 optimal weight:   20.0000
   chunk 74 optimal weight:    0.0010
   chunk 0 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8361  Z= 0.153
  Angle     :  0.499   7.355  11440  Z= 0.262
  Chirality :  0.039   0.132   1367
  Planarity :  0.003   0.040   1450
  Dihedral  :  3.945  29.688   1267
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.59 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.84 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.45 (0.26), residues: 1115
  helix:  2.53 (0.28), residues: 363
  sheet:  0.03 (0.31), residues: 291
  loop : -1.41 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.003   0.001   HIS E 107 
 PHE   0.011   0.001   PHE B  74 
 TYR   0.010   0.001   TYR B 115 
 ARG   0.006   0.000   ARG D  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7384 (mttp)
REVERT: A  151 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8090 (m-80)
REVERT: A  228 ASP cc_start: 0.7690 (m-30) cc_final: 0.7210 (m-30)
REVERT: A  254 ASP cc_start: 0.8552 (t0) cc_final: 0.7776 (m-30)
REVERT: A  259 GLN cc_start: 0.8114 (pt0) cc_final: 0.7899 (pt0)
REVERT: B   43 ASN cc_start: 0.7571 (t0) cc_final: 0.7175 (t0)
REVERT: B  111 ASP cc_start: 0.8481 (t0) cc_final: 0.8005 (t0)
REVERT: B  113 SER cc_start: 0.8776 (t) cc_final: 0.8507 (p)
REVERT: B  167 PHE cc_start: 0.7671 (t80) cc_final: 0.7313 (t80)
REVERT: F   19 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8095 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 159
  average time/residue: 0.1721
  time to fit residues: 38.8158
Evaluate side-chains
  158 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain F residue   19 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0030
   chunk 26 optimal weight:    6.9990
   chunk 108 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.9594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8361  Z= 0.147
  Angle     :  0.495   8.542  11440  Z= 0.260
  Chirality :  0.039   0.132   1367
  Planarity :  0.003   0.039   1450
  Dihedral  :  3.872  29.288   1267
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.50 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.49 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.46 (0.26), residues: 1115
  helix:  2.57 (0.28), residues: 363
  sheet:  0.11 (0.31), residues: 288
  loop : -1.47 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 129 
 HIS   0.004   0.001   HIS E 107 
 PHE   0.011   0.001   PHE B  74 
 TYR   0.010   0.001   TYR B 115 
 ARG   0.007   0.000   ARG D  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A   57 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7367 (mttp)
REVERT: A  151 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8074 (m-80)
REVERT: A  228 ASP cc_start: 0.7677 (m-30) cc_final: 0.7202 (m-30)
REVERT: A  254 ASP cc_start: 0.8560 (t0) cc_final: 0.7770 (m-30)
REVERT: B   43 ASN cc_start: 0.7534 (t0) cc_final: 0.7157 (t0)
REVERT: B   85 ASP cc_start: 0.7563 (p0) cc_final: 0.7341 (p0)
REVERT: B  167 PHE cc_start: 0.7685 (t80) cc_final: 0.7370 (t80)
REVERT: B  188 ARG cc_start: 0.7341 (ttt90) cc_final: 0.6079 (tpp80)
REVERT: D  159 ASN cc_start: 0.8906 (m110) cc_final: 0.8616 (m110)
REVERT: D  221 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (tt)
REVERT: F   19 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8114 (tt)
  outliers start: 21
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1772
  time to fit residues: 39.4326
Evaluate side-chains
  156 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain F residue   19 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 107 optimal weight:    0.0060
   chunk 67 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 49 optimal weight:    8.9990
   chunk 66 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.9202

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8361  Z= 0.149
  Angle     :  0.500   9.784  11440  Z= 0.261
  Chirality :  0.039   0.132   1367
  Planarity :  0.003   0.039   1450
  Dihedral  :  3.806  29.052   1267
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.27 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.52 (0.26), residues: 1115
  helix:  2.59 (0.28), residues: 364
  sheet:  0.18 (0.32), residues: 281
  loop : -1.43 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 129 
 HIS   0.004   0.001   HIS E 107 
 PHE   0.010   0.001   PHE B  74 
 TYR   0.010   0.001   TYR B 115 
 ARG   0.006   0.000   ARG D  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7288 (mttp)
REVERT: A  151 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8088 (m-80)
REVERT: A  228 ASP cc_start: 0.7680 (m-30) cc_final: 0.7194 (m-30)
REVERT: A  254 ASP cc_start: 0.8532 (t0) cc_final: 0.7720 (m-30)
REVERT: B   43 ASN cc_start: 0.7529 (t0) cc_final: 0.7135 (t0)
REVERT: B  111 ASP cc_start: 0.8417 (t0) cc_final: 0.8019 (t0)
REVERT: B  167 PHE cc_start: 0.7665 (t80) cc_final: 0.7359 (t80)
REVERT: B  188 ARG cc_start: 0.7372 (ttt90) cc_final: 0.6328 (tpt170)
REVERT: D  159 ASN cc_start: 0.8902 (m110) cc_final: 0.8574 (m110)
REVERT: D  221 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (tt)
REVERT: F   19 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8112 (tt)
  outliers start: 19
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1664
  time to fit residues: 35.4999
Evaluate side-chains
  158 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain F residue   19 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0370
   chunk 73 optimal weight:    0.6980
   chunk 53 optimal weight:    9.9990
   chunk 10 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.7460

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8361  Z= 0.141
  Angle     :  0.496  10.955  11440  Z= 0.258
  Chirality :  0.039   0.131   1367
  Planarity :  0.003   0.039   1450
  Dihedral  :  3.736  28.870   1267
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.52 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.26), residues: 1115
  helix:  2.63 (0.28), residues: 365
  sheet:  0.17 (0.32), residues: 284
  loop : -1.51 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 129 
 HIS   0.004   0.001   HIS E 107 
 PHE   0.011   0.001   PHE B  74 
 TYR   0.009   0.001   TYR B 115 
 ARG   0.007   0.000   ARG D  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A   57 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7334 (mttp)
REVERT: A  151 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.8051 (m-80)
REVERT: A  228 ASP cc_start: 0.7724 (m-30) cc_final: 0.7250 (m-30)
REVERT: A  254 ASP cc_start: 0.8519 (t0) cc_final: 0.7694 (m-30)
REVERT: B   43 ASN cc_start: 0.7542 (t0) cc_final: 0.7138 (t0)
REVERT: B   77 ASP cc_start: 0.8391 (t0) cc_final: 0.8174 (t0)
REVERT: B  111 ASP cc_start: 0.8390 (t0) cc_final: 0.7998 (t0)
REVERT: B  167 PHE cc_start: 0.7614 (t80) cc_final: 0.7310 (t80)
REVERT: B  188 ARG cc_start: 0.7305 (ttt90) cc_final: 0.6076 (tpp80)
REVERT: D  159 ASN cc_start: 0.8899 (m110) cc_final: 0.8576 (m110)
REVERT: D  221 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8461 (tt)
REVERT: E  284 ILE cc_start: 0.7834 (pt) cc_final: 0.7629 (pt)
REVERT: F   19 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8103 (tt)
  outliers start: 21
  outliers final: 14
  residues processed: 155
  average time/residue: 0.1698
  time to fit residues: 37.5679
Evaluate side-chains
  160 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  299 VAL
Chi-restraints excluded: chain F residue   19 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:   30.0000
   chunk 100 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.9342

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8361  Z= 0.154
  Angle     :  0.513  11.430  11440  Z= 0.266
  Chirality :  0.039   0.131   1367
  Planarity :  0.003   0.038   1450
  Dihedral  :  3.742  28.596   1267
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.78 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.52 (0.26), residues: 1115
  helix:  2.61 (0.28), residues: 366
  sheet:  0.18 (0.31), residues: 287
  loop : -1.49 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 129 
 HIS   0.004   0.001   HIS E 107 
 PHE   0.011   0.001   PHE B  74 
 TYR   0.013   0.001   TYR E  81 
 ARG   0.006   0.000   ARG D  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   57 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7356 (mttp)
REVERT: A  151 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.8082 (m-80)
REVERT: A  228 ASP cc_start: 0.7696 (m-30) cc_final: 0.7199 (m-30)
REVERT: A  254 ASP cc_start: 0.8528 (t0) cc_final: 0.7692 (m-30)
REVERT: B   43 ASN cc_start: 0.7522 (t0) cc_final: 0.7307 (t0)
REVERT: B   77 ASP cc_start: 0.8388 (t0) cc_final: 0.8174 (t0)
REVERT: B  167 PHE cc_start: 0.7607 (t80) cc_final: 0.7295 (t80)
REVERT: B  188 ARG cc_start: 0.7333 (ttt90) cc_final: 0.6114 (tpp80)
REVERT: D  159 ASN cc_start: 0.8929 (m110) cc_final: 0.8589 (m110)
REVERT: D  221 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8463 (tt)
REVERT: E  284 ILE cc_start: 0.7794 (pt) cc_final: 0.7591 (pt)
  outliers start: 21
  outliers final: 15
  residues processed: 151
  average time/residue: 0.1864
  time to fit residues: 39.9067
Evaluate side-chains
  155 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   79 ASN
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   chunk 102 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 9 optimal weight:    0.3980
   chunk 68 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 94 optimal weight:   30.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8361  Z= 0.144
  Angle     :  0.500  11.816  11440  Z= 0.260
  Chirality :  0.039   0.131   1367
  Planarity :  0.003   0.038   1450
  Dihedral  :  3.688  28.406   1267
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.04 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.58 (0.26), residues: 1115
  helix:  2.74 (0.28), residues: 362
  sheet:  0.24 (0.32), residues: 284
  loop : -1.51 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 129 
 HIS   0.004   0.001   HIS E 107 
 PHE   0.011   0.001   PHE B  74 
 TYR   0.009   0.001   TYR B 115 
 ARG   0.001   0.000   ARG A  68 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A   57 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7319 (mttp)
REVERT: A  151 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.8045 (m-80)
REVERT: A  228 ASP cc_start: 0.7704 (m-30) cc_final: 0.7214 (m-30)
REVERT: A  254 ASP cc_start: 0.8538 (t0) cc_final: 0.7712 (m-30)
REVERT: A  301 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8407 (mmtt)
REVERT: B   43 ASN cc_start: 0.7505 (t0) cc_final: 0.7294 (t0)
REVERT: B  111 ASP cc_start: 0.8365 (t0) cc_final: 0.8126 (t0)
REVERT: B  167 PHE cc_start: 0.7598 (t80) cc_final: 0.7293 (t80)
REVERT: B  188 ARG cc_start: 0.7304 (ttt90) cc_final: 0.6098 (tpp80)
REVERT: D  159 ASN cc_start: 0.8929 (m110) cc_final: 0.8576 (m110)
REVERT: D  221 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8448 (tt)
  outliers start: 21
  outliers final: 17
  residues processed: 142
  average time/residue: 0.1627
  time to fit residues: 33.4195
Evaluate side-chains
  153 residues out of total 979 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  244 ASN
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   74 ASP
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain E residue   79 ASN
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue  107 HIS
Chi-restraints excluded: chain E residue  278 SER
Chi-restraints excluded: chain E residue  299 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
F  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.153664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.113892 restraints weight = 13992.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 3.75
r_work: 0.3355 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8361  Z= 0.179
  Angle     :  0.526  12.018  11440  Z= 0.272
  Chirality :  0.039   0.139   1367
  Planarity :  0.003   0.038   1450
  Dihedral  :  3.760  28.117   1267
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.17 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.52 (0.26), residues: 1115
  helix:  2.74 (0.28), residues: 360
  sheet:  0.21 (0.32), residues: 281
  loop : -1.55 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 129 
 HIS   0.004   0.001   HIS E 107 
 PHE   0.010   0.001   PHE B  74 
 TYR   0.009   0.001   TYR D 178 
 ARG   0.001   0.000   ARG D  18 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2238.63 seconds
wall clock time: 40 minutes 52.68 seconds (2452.68 seconds total)