Starting phenix.real_space_refine
on Wed Jul 30 00:55:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o14_12689/07_2025/7o14_12689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o14_12689/07_2025/7o14_12689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o14_12689/07_2025/7o14_12689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o14_12689/07_2025/7o14_12689.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o14_12689/07_2025/7o14_12689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o14_12689/07_2025/7o14_12689.cif"
  }
  resolution = 3.8
  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: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      36      5.16       5
     C    7545      2.51       5
     N    2069      2.21       5
     O    2136      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11787
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2367
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 12, 'TRANS': 294}
    Chain: "C"
      Number of atoms: 2367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2367
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 12, 'TRANS': 294}
    Chain: "D"
      Number of atoms: 2015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2015
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 8, 'TRANS': 258}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1896
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 8, 'TRANS': 239}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 3140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3140
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 16, 'TRANS': 385}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 7.17, per 1000 atoms: 0.61
  Number of scatterers: 11787
  At special positions: 0
  Unit cell: (75.168, 90.72, 195.696, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     Mg      1     11.99
     O    2136      8.00
     N    2069      7.00
     C    7545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.06
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2752

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 12 sheets defined
      46.4% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'B' and resid 41 through 50
      removed outlier: 4.087A  pdb=" N   SER B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B  50 " --> pdb=" O   MET B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
      removed outlier: 3.528A  pdb=" N   ARG B  74 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 103
      removed outlier: 3.526A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG B 100 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 101 " --> pdb=" O   HIS B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 116
      removed outlier: 4.403A  pdb=" N   ASP B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 160 through 178
    Processing helix  chain 'B' and resid 211 through 219
    Processing helix  chain 'B' and resid 234 through 242
      removed outlier: 4.430A  pdb=" N   TRP B 240 " --> pdb=" O   TRP B 236 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   THR B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 273
      removed outlier: 3.739A  pdb=" N   ARG B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   GLN B 270 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 299
    Processing helix  chain 'C' and resid 41 through 50
      removed outlier: 3.774A  pdb=" N   SER C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS C  47 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU C  50 " --> pdb=" O   MET C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 75
      removed outlier: 3.993A  pdb=" N   GLN C  75 " --> pdb=" O   GLN C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 103
      removed outlier: 3.677A  pdb=" N   LEU C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 116
      removed outlier: 4.001A  pdb=" N   GLU C 111 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 129
    Processing helix  chain 'C' and resid 130 through 141
      removed outlier: 3.544A  pdb=" N   ARG C 134 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 177
      removed outlier: 3.577A  pdb=" N   TYR C 168 " --> pdb=" O   THR C 164 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU C 169 " --> pdb=" O   GLN C 165 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 4.018A  pdb=" N   ALA C 193 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 219
      removed outlier: 3.586A  pdb=" N   ARG C 216 " --> pdb=" O   LEU C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 238
      removed outlier: 4.010A  pdb=" N   TRP C 236 " --> pdb=" O   GLU C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
      removed outlier: 4.039A  pdb=" N   GLN C 270 " --> pdb=" O   VAL C 266 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C 271 " --> pdb=" O   LEU C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 298
      removed outlier: 3.502A  pdb=" N   MET C 295 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 4.082A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   SER D  13 " --> pdb=" O   ARG D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.564A  pdb=" N   ILE D  24 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA D  36 " --> pdb=" O   ALA D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.687A  pdb=" N   ILE D  55 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.615A  pdb=" N   TYR D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.750A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 3.932A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY D 119 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 167
      removed outlier: 3.564A  pdb=" N   SER D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.611A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
      removed outlier: 3.535A  pdb=" N   SER D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 215
      removed outlier: 3.522A  pdb=" N   LEU D 215 " --> pdb=" O   LEU D 212 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 216 through 226
      removed outlier: 3.533A  pdb=" N   ASN D 225 " --> pdb=" O   TYR D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 245
      removed outlier: 3.680A  pdb=" N   LEU D 241 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA D 243 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.749A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE D 260 " --> pdb=" O   LEU D 256 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
      removed outlier: 3.598A  pdb=" N   ILE E   7 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 3 through 7'
    Processing helix  chain 'E' and resid 7 through 16
      removed outlier: 3.549A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER E  13 " --> pdb=" O   ARG E   9 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.573A  pdb=" N   ALA E  36 " --> pdb=" O   ALA E  32 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.888A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE E  64 " --> pdb=" O   SER E  60 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   MET E  66 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
      removed outlier: 3.502A  pdb=" N   TYR E  75 " --> pdb=" O   LEU E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 84
    Processing helix  chain 'E' and resid 85 through 91
      removed outlier: 3.542A  pdb=" N   LEU E  89 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.559A  pdb=" N   ILE E 100 " --> pdb=" O   GLY E  96 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU E 101 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 129
    Processing helix  chain 'E' and resid 135 through 143
      removed outlier: 3.836A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
      removed outlier: 3.629A  pdb=" N   VAL E 168 " --> pdb=" O   LEU E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.503A  pdb=" N   ALA E 175 " --> pdb=" O   LYS E 171 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
      removed outlier: 3.528A  pdb=" N   LEU E 199 " --> pdb=" O   ALA E 195 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 213
      removed outlier: 3.522A  pdb=" N   LEU E 212 " --> pdb=" O   LEU E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.552A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 4.032A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.750A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   TRP A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 390
    Processing helix  chain 'A' and resid 392 through 405
      removed outlier: 3.919A  pdb=" N   GLN A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.613A  pdb=" N   VAL B   4 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 9 through 12
      removed outlier: 7.783A  pdb=" N   GLN B  11 " --> pdb=" O   HIS B  20 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   HIS B  20 " --> pdb=" O   GLN B  11 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 153
      removed outlier: 6.274A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   VAL B  31 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   ALA B 199 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   GLY B  33 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 247 through 250
      removed outlier: 3.675A  pdb=" N   SER B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 24
      removed outlier: 6.281A  pdb=" N   HIS C  20 " --> pdb=" O   SER C  10 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   SER C  10 " --> pdb=" O   HIS C  20 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN C  59 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 149 through 152
      removed outlier: 3.551A  pdb=" N   ILE C 182 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 247 through 249
      removed outlier: 3.586A  pdb=" N   GLU C 256 " --> pdb=" O   ARG C 248 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 37 through 40
      removed outlier: 8.090A  pdb=" N   ARG A  44 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   TRP A  45 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 52 through 53
      removed outlier: 6.741A  pdb=" N   ILE A  72 " --> pdb=" O   TYR A  96 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ILE A 199 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   THR A 221 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL A 266 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.507A  pdb=" N   GLY A 131 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ILE A 251 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   TYR A 291 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   MET A 253 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU A 288 " --> pdb=" O   HIS A 311 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   GLN A 332 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 89 through 91
      removed outlier: 6.575A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL A 142 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 215 through 217
      removed outlier: 7.569A  pdb=" N   SER A 322 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ILE A 298 " --> pdb=" O   SER A 322 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1374 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: 4.06

  Time building geometry restraints manager: 3.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3633
        1.33 -     1.45: 1919
        1.45 -     1.57: 6390
        1.57 -     1.69: 3
        1.69 -     1.81: 62
  Bond restraints: 12007
  Sorted by residual:
  bond pdb=" CA  ILE E  51 "
       pdb=" C   ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.525  1.591 -0.066 2.10e-02 2.27e+03 1.00e+01
  bond pdb=" CB  THR E 218 "
       pdb=" CG2 THR E 218 "
    ideal  model  delta    sigma   weight residual
    1.521  1.429  0.092 3.30e-02 9.18e+02 7.75e+00
  bond pdb=" CB  ASN B 261 "
       pdb=" CG  ASN B 261 "
    ideal  model  delta    sigma   weight residual
    1.516  1.583 -0.067 2.50e-02 1.60e+03 7.24e+00
  bond pdb=" CB  THR E  63 "
       pdb=" CG2 THR E  63 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.63e+00
  bond pdb=" CG1 ILE B 181 "
       pdb=" CD1 ILE B 181 "
    ideal  model  delta    sigma   weight residual
    1.513  1.423  0.090 3.90e-02 6.57e+02 5.35e+00
  ... (remaining 12002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 15989
        3.61 -     7.21: 269
        7.21 -    10.82: 35
       10.82 -    14.43: 4
       14.43 -    18.03: 1
  Bond angle restraints: 16298
  Sorted by residual:
  angle pdb=" C   SER B 231 "
        pdb=" N   GLU B 232 "
        pdb=" CA  GLU B 232 "
      ideal   model   delta    sigma   weight residual
     121.54  133.86  -12.32 1.91e+00 2.74e-01 4.16e+01
  angle pdb=" CA  ASN B  82 "
        pdb=" CB  ASN B  82 "
        pdb=" CG  ASN B  82 "
      ideal   model   delta    sigma   weight residual
     112.60  118.11   -5.51 1.00e+00 1.00e+00 3.03e+01
  angle pdb=" CA  ASN B 261 "
        pdb=" CB  ASN B 261 "
        pdb=" CG  ASN B 261 "
      ideal   model   delta    sigma   weight residual
     112.60  117.95   -5.35 1.00e+00 1.00e+00 2.86e+01
  angle pdb=" CA  VAL E 186 "
        pdb=" CB  VAL E 186 "
        pdb=" CG1 VAL E 186 "
      ideal   model   delta    sigma   weight residual
     110.40  119.31   -8.91 1.70e+00 3.46e-01 2.75e+01
  angle pdb=" CA  LEU A  35 "
        pdb=" CB  LEU A  35 "
        pdb=" CG  LEU A  35 "
      ideal   model   delta    sigma   weight residual
     116.30  134.33  -18.03 3.50e+00 8.16e-02 2.66e+01
  ... (remaining 16293 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.27: 6142
       15.27 -    30.53: 730
       30.53 -    45.80: 197
       45.80 -    61.07: 30
       61.07 -    76.33: 8
  Dihedral angle restraints: 7107
    sinusoidal: 2791
      harmonic: 4316
  Sorted by residual:
  dihedral pdb=" CA  GLU B 232 "
           pdb=" C   GLU B 232 "
           pdb=" N   ARG B 233 "
           pdb=" CA  ARG B 233 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.25   33.75     0      5.00e+00 4.00e-02 4.56e+01
  dihedral pdb=" CA  GLN B 304 "
           pdb=" C   GLN B 304 "
           pdb=" N   GLU B 305 "
           pdb=" CA  GLU B 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.18  -32.82     0      5.00e+00 4.00e-02 4.31e+01
  dihedral pdb=" CA  GLU B 305 "
           pdb=" C   GLU B 305 "
           pdb=" N   GLY B 306 "
           pdb=" CA  GLY B 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.19   29.81     0      5.00e+00 4.00e-02 3.55e+01
  ... (remaining 7104 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1639
       0.096 -    0.192: 203
       0.192 -    0.288: 29
       0.288 -    0.384: 7
       0.384 -    0.480: 2
  Chirality restraints: 1880
  Sorted by residual:
  chirality pdb=" CB  VAL A 413 "
            pdb=" CA  VAL A 413 "
            pdb=" CG1 VAL A 413 "
            pdb=" CG2 VAL A 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.15   -0.48 2.00e-01 2.50e+01 5.75e+00
  chirality pdb=" CB  ILE A 321 "
            pdb=" CA  ILE A 321 "
            pdb=" CG1 ILE A 321 "
            pdb=" CG2 ILE A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.47 2.00e-01 2.50e+01 5.55e+00
  chirality pdb=" CA  ASN B  82 "
            pdb=" N   ASN B  82 "
            pdb=" C   ASN B  82 "
            pdb=" CB  ASN B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.79e+00
  ... (remaining 1877 not shown)

  Planarity restraints: 2090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  81 "   -0.018 2.00e-02 2.50e+03   3.76e-02 1.42e+01
        pdb=" C   GLU B  81 "    0.065 2.00e-02 2.50e+03
        pdb=" O   GLU B  81 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ASN B  82 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 345 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   VAL A 345 "    0.057 2.00e-02 2.50e+03
        pdb=" O   VAL A 345 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ASP A 346 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "   -0.051 5.00e-02 4.00e+02   7.53e-02 9.06e+00
        pdb=" N   PRO D  67 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "   -0.043 5.00e-02 4.00e+02
  ... (remaining 2087 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 20
        2.39 -     3.02: 5875
        3.02 -     3.65: 17980
        3.65 -     4.27: 27159
        4.27 -     4.90: 44640
  Nonbonded interactions: 95674
  Sorted by model distance:
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     1.764 2.170
  nonbonded pdb=" OD1 ASP A 359 "
            pdb="MG    MG A 501 "
     model   vdw
     1.990 2.170
  nonbonded pdb=" OD1 ASN A 361 "
            pdb="MG    MG A 501 "
     model   vdw
     2.137 2.170
  nonbonded pdb=" OD1 ASP A 363 "
            pdb="MG    MG A 501 "
     model   vdw
     2.161 2.170
  nonbonded pdb=" OD1 ASN A 361 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.270 3.040
  ... (remaining 95669 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through  \ 
274))
  selection = chain 'E'
}

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 group one per residue
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:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     30.210
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
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      :  0.009   0.109  12007  Z= 0.390
  Angle     :  1.162  18.035  16298  Z= 0.616
  Chirality :  0.070   0.480   1880
  Planarity :  0.008   0.075   2090
  Dihedral  : 14.286  76.335   4355
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  8.89 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -5.80 (0.14), residues: 1515
  helix: -4.51 (0.07), residues: 650
  sheet: -3.42 (0.25), residues: 226
  loop : -3.03 (0.19), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 155 
 HIS   0.012   0.002   HIS C 194 
 PHE   0.019   0.003   PHE A  56 
 TYR   0.018   0.003   TYR A 204 
 ARG   0.023   0.002   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30803 (  483)
  hydrogen bonds       : angle      10.86637 ( 1374)
  covalent geometry    : bond        0.00879 (12007)
  covalent geometry    : angle       1.16165 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
REVERT: B  304 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8362 (mt0)
REVERT: C  133 MET cc_start: 0.8981 (mtm) cc_final: 0.8725 (mtm)
REVERT: C  181 ILE cc_start: 0.9270 (mt) cc_final: 0.9066 (mm)
REVERT: D   66 MET cc_start: 0.9100 (mmm) cc_final: 0.8882 (mmm)
REVERT: D  117 LEU cc_start: 0.9266 (tp) cc_final: 0.9023 (tt)
REVERT: E  147 MET cc_start: 0.8813 (mtt) cc_final: 0.8522 (mmm)
REVERT: A  209 MET cc_start: 0.9010 (mmm) cc_final: 0.8709 (mmm)
REVERT: A  231 MET cc_start: 0.8862 (mtt) cc_final: 0.8226 (mtt)
REVERT: A  305 LYS cc_start: 0.9356 (mmtt) cc_final: 0.8691 (mmmm)
  outliers start: 9
  outliers final: 2
  residues processed: 105
  average time/residue: 0.2803
  time to fit residues: 40.7397
Evaluate side-chains
  61 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    5.9990
   chunk 113 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 136 optimal weight:    6.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
B   2 ASN
B  23 ASN
B 207 GLN
C 194 HIS
C 270 GLN
D 205 ASN
D 225 ASN
E 108 HIS
E 225 ASN
A  63 GLN
A  77 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
A 174 HIS
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 HIS
A 179 ASN
A 190 ASN
A 212 ASN
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 341 GLN
A 417 HIS

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.048420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.037437 restraints weight = 60119.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.038791 restraints weight = 31189.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.039712 restraints weight = 20224.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12007  Z= 0.154
  Angle     :  0.620   9.496  16298  Z= 0.324
  Chirality :  0.043   0.178   1880
  Planarity :  0.005   0.042   2090
  Dihedral  :  5.211  33.630   1665
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.02 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.63 (0.18), residues: 1515
  helix: -1.97 (0.16), residues: 668
  sheet: -2.83 (0.28), residues: 227
  loop : -2.56 (0.22), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 253 
 HIS   0.004   0.001   HIS A 417 
 PHE   0.011   0.001   PHE D 157 
 TYR   0.016   0.001   TYR B  86 
 ARG   0.003   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  483)
  hydrogen bonds       : angle       5.13163 ( 1374)
  covalent geometry    : bond        0.00325 (12007)
  covalent geometry    : angle       0.61996 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  304 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9002 (mm-40)
REVERT: E  138 MET cc_start: 0.8065 (tmm) cc_final: 0.7757 (tmm)
REVERT: A  209 MET cc_start: 0.8865 (mmm) cc_final: 0.8625 (mmm)
REVERT: A  231 MET cc_start: 0.8785 (mtt) cc_final: 0.8030 (mtt)
REVERT: A  305 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8519 (mmmm)
  outliers start: 21
  outliers final: 12
  residues processed: 81
  average time/residue: 0.2461
  time to fit residues: 29.5051
Evaluate side-chains
  67 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue  183 PHE
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  286 LYS
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 130 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 111 optimal weight:    9.9990
   chunk 103 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 134 optimal weight:   20.0000
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 245 HIS
C  25 ASN
C 176 GLN
A  30 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 HIS
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.048285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.037341 restraints weight = 60947.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.038656 restraints weight = 32255.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.039553 restraints weight = 21147.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12007  Z= 0.168
  Angle     :  0.599   8.585  16298  Z= 0.307
  Chirality :  0.043   0.181   1880
  Planarity :  0.004   0.034   2090
  Dihedral  :  4.847  32.368   1665
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.20 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.29 (0.20), residues: 1515
  helix: -0.39 (0.20), residues: 669
  sheet: -2.56 (0.30), residues: 233
  loop : -2.29 (0.23), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 141 
 HIS   0.003   0.001   HIS B  37 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.014   0.001   TYR B 291 
 ARG   0.003   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03411 (  483)
  hydrogen bonds       : angle       4.57951 ( 1374)
  covalent geometry    : bond        0.00369 (12007)
  covalent geometry    : angle       0.59915 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  138 MET cc_start: 0.8180 (tmm) cc_final: 0.7828 (tmm)
REVERT: E  147 MET cc_start: 0.8592 (mmm) cc_final: 0.8165 (mmt)
REVERT: A  125 MET cc_start: 0.9071 (mpp) cc_final: 0.8441 (mpp)
REVERT: A  137 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.9032 (m)
REVERT: A  209 MET cc_start: 0.8885 (mmm) cc_final: 0.8334 (mmm)
REVERT: A  231 MET cc_start: 0.8949 (mtt) cc_final: 0.8271 (mtm)
REVERT: A  305 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8517 (mmmm)
  outliers start: 22
  outliers final: 14
  residues processed: 74
  average time/residue: 0.2560
  time to fit residues: 28.8488
Evaluate side-chains
  65 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 148 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 120 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 111 optimal weight:    9.9990
   chunk 129 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.046505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.035718 restraints weight = 62093.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.036969 restraints weight = 33377.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.037825 restraints weight = 22112.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  12007  Z= 0.272
  Angle     :  0.683   8.418  16298  Z= 0.343
  Chirality :  0.045   0.183   1880
  Planarity :  0.004   0.033   2090
  Dihedral  :  4.930  30.726   1665
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.33 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.80 (0.21), residues: 1515
  helix:  0.27 (0.20), residues: 672
  sheet: -2.61 (0.29), residues: 243
  loop : -2.22 (0.23), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 259 
 HIS   0.004   0.001   HIS C 194 
 PHE   0.014   0.002   PHE D 157 
 TYR   0.017   0.002   TYR B 291 
 ARG   0.005   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (  483)
  hydrogen bonds       : angle       4.69314 ( 1374)
  covalent geometry    : bond        0.00591 (12007)
  covalent geometry    : angle       0.68278 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 47
  time to evaluate  : 1.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8668 (pp)
REVERT: B  304 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8474 (mt0)
REVERT: C   37 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.5446 (p-80)
REVERT: C  295 MET cc_start: 0.9345 (mmm) cc_final: 0.9067 (mmm)
REVERT: E   83 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: E   88 MET cc_start: 0.8629 (tpp) cc_final: 0.8347 (tpp)
REVERT: E  138 MET cc_start: 0.8088 (tmm) cc_final: 0.7783 (tmm)
REVERT: A   62 MET cc_start: 0.8385 (tpt) cc_final: 0.8144 (tpt)
REVERT: A  125 MET cc_start: 0.9026 (mpp) cc_final: 0.8230 (mpp)
REVERT: A  231 MET cc_start: 0.8902 (mtt) cc_final: 0.8582 (mtt)
  outliers start: 35
  outliers final: 24
  residues processed: 80
  average time/residue: 0.2088
  time to fit residues: 26.4954
Evaluate side-chains
  73 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 47
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain D residue  164 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain A residue   38 GLN
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 112 optimal weight:   20.0000
   chunk 11 optimal weight:    0.2980
   chunk 92 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 86 optimal weight:    7.9990
   chunk 74 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
C  97 HIS
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.048356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.037604 restraints weight = 59693.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.038903 restraints weight = 31821.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.039786 restraints weight = 20864.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  12007  Z= 0.109
  Angle     :  0.539   9.720  16298  Z= 0.275
  Chirality :  0.042   0.183   1880
  Planarity :  0.003   0.032   2090
  Dihedral  :  4.571  30.563   1665
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.06 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.23 (0.22), residues: 1515
  helix:  0.81 (0.21), residues: 678
  sheet: -2.34 (0.30), residues: 242
  loop : -2.04 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 253 
 HIS   0.003   0.001   HIS B  37 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.013   0.001   TYR D 221 
 ARG   0.003   0.000   ARG D 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02849 (  483)
  hydrogen bonds       : angle       4.16679 ( 1374)
  covalent geometry    : bond        0.00241 (12007)
  covalent geometry    : angle       0.53924 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 56
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8666 (pp)
REVERT: B  276 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.5870 (pp20)
REVERT: C   37 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.5649 (p-80)
REVERT: C   79 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8707 (tt)
REVERT: C  133 MET cc_start: 0.8795 (mtm) cc_final: 0.8439 (ptp)
REVERT: C  295 MET cc_start: 0.9291 (mmm) cc_final: 0.9034 (mmm)
REVERT: E   83 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8412 (mm-30)
REVERT: E   88 MET cc_start: 0.8554 (tpp) cc_final: 0.8221 (tpp)
REVERT: E  138 MET cc_start: 0.8089 (tmm) cc_final: 0.7811 (tmm)
REVERT: E  147 MET cc_start: 0.8566 (mmm) cc_final: 0.8153 (mmt)
REVERT: E  186 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8957 (p)
REVERT: A   62 MET cc_start: 0.8382 (tpt) cc_final: 0.8121 (tpt)
REVERT: A  125 MET cc_start: 0.9048 (mpp) cc_final: 0.8257 (mpp)
REVERT: A  137 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8990 (m)
REVERT: A  209 MET cc_start: 0.9056 (mmm) cc_final: 0.8790 (mmm)
REVERT: A  231 MET cc_start: 0.9058 (mtt) cc_final: 0.8407 (mtt)
  outliers start: 39
  outliers final: 18
  residues processed: 90
  average time/residue: 0.1982
  time to fit residues: 28.0368
Evaluate side-chains
  75 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 51
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 139 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0670
   chunk 79 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.049225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.038357 restraints weight = 60665.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.039724 restraints weight = 32074.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.040630 restraints weight = 20887.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12007  Z= 0.092
  Angle     :  0.535   9.142  16298  Z= 0.268
  Chirality :  0.042   0.182   1880
  Planarity :  0.003   0.032   2090
  Dihedral  :  4.350  30.888   1665
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.03 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.83 (0.22), residues: 1515
  helix:  1.24 (0.21), residues: 672
  sheet: -2.17 (0.31), residues: 242
  loop : -1.91 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  45 
 HIS   0.003   0.001   HIS B  37 
 PHE   0.011   0.001   PHE E  64 
 TYR   0.016   0.001   TYR C  13 
 ARG   0.003   0.000   ARG D 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02703 (  483)
  hydrogen bonds       : angle       3.90174 ( 1374)
  covalent geometry    : bond        0.00203 (12007)
  covalent geometry    : angle       0.53541 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8545 (pp)
REVERT: B  276 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.5921 (pp20)
REVERT: C   79 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8680 (tt)
REVERT: C  133 MET cc_start: 0.8741 (mtm) cc_final: 0.8387 (ptp)
REVERT: E   83 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8370 (mt-10)
REVERT: E   88 MET cc_start: 0.8479 (tpp) cc_final: 0.8144 (tpp)
REVERT: E  138 MET cc_start: 0.8129 (tmm) cc_final: 0.7829 (tmm)
REVERT: E  147 MET cc_start: 0.8533 (mmm) cc_final: 0.8156 (mmt)
REVERT: E  186 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8956 (p)
REVERT: A   62 MET cc_start: 0.8405 (tpt) cc_final: 0.8167 (tpt)
REVERT: A   81 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9173 (mm)
REVERT: A  125 MET cc_start: 0.9034 (mpp) cc_final: 0.8260 (mpp)
REVERT: A  209 MET cc_start: 0.8935 (mmm) cc_final: 0.8679 (mmm)
REVERT: A  231 MET cc_start: 0.8830 (mtt) cc_final: 0.8140 (mtt)
REVERT: A  305 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8523 (mmmt)
  outliers start: 26
  outliers final: 15
  residues processed: 75
  average time/residue: 0.1870
  time to fit residues: 22.9555
Evaluate side-chains
  71 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 51
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 139 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 134 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.047883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.036866 restraints weight = 62015.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.038176 restraints weight = 33371.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.039049 restraints weight = 22121.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12007  Z= 0.162
  Angle     :  0.576   8.527  16298  Z= 0.287
  Chirality :  0.043   0.240   1880
  Planarity :  0.003   0.030   2090
  Dihedral  :  4.408  29.282   1665
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.27 %
    Favored  : 79.55 %
  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 (0.22), residues: 1515
  helix:  1.34 (0.21), residues: 677
  sheet: -2.00 (0.31), residues: 252
  loop : -1.94 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  45 
 HIS   0.003   0.001   HIS C 194 
 PHE   0.011   0.001   PHE E  64 
 TYR   0.015   0.001   TYR C  13 
 ARG   0.003   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02904 (  483)
  hydrogen bonds       : angle       4.09337 ( 1374)
  covalent geometry    : bond        0.00359 (12007)
  covalent geometry    : angle       0.57605 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 52
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8571 (pp)
REVERT: C   37 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.5790 (p-80)
REVERT: C   79 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8737 (tt)
REVERT: C  133 MET cc_start: 0.8864 (mtm) cc_final: 0.8387 (ptp)
REVERT: C  272 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: C  295 MET cc_start: 0.9233 (mmp) cc_final: 0.8824 (mmm)
REVERT: E   88 MET cc_start: 0.8552 (tpp) cc_final: 0.8195 (tpp)
REVERT: E  138 MET cc_start: 0.8088 (tmm) cc_final: 0.7816 (tmm)
REVERT: E  147 MET cc_start: 0.8556 (mmm) cc_final: 0.8152 (mmt)
REVERT: E  186 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9006 (p)
REVERT: A  125 MET cc_start: 0.9029 (mpp) cc_final: 0.8342 (mpp)
REVERT: A  137 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8883 (m)
REVERT: A  209 MET cc_start: 0.8961 (mmm) cc_final: 0.8736 (mmm)
REVERT: A  231 MET cc_start: 0.8684 (mtt) cc_final: 0.7719 (mtt)
  outliers start: 27
  outliers final: 18
  residues processed: 78
  average time/residue: 0.2219
  time to fit residues: 27.8698
Evaluate side-chains
  73 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 49
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 113 optimal weight:   20.0000
   chunk 131 optimal weight:    9.9990
   chunk 149 optimal weight:    4.9990
   chunk 133 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 144 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 111 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.047986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.037002 restraints weight = 61248.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.038302 restraints weight = 33050.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.039167 restraints weight = 21972.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12007  Z= 0.150
  Angle     :  0.569   8.917  16298  Z= 0.283
  Chirality :  0.042   0.236   1880
  Planarity :  0.003   0.029   2090
  Dihedral  :  4.396  28.998   1665
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.35 %
    Favored  : 79.39 %
  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: -0.63 (0.22), residues: 1515
  helix:  1.44 (0.21), residues: 677
  sheet: -2.01 (0.31), residues: 255
  loop : -1.90 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  45 
 HIS   0.003   0.001   HIS C  37 
 PHE   0.011   0.001   PHE E  64 
 TYR   0.020   0.001   TYR D 221 
 ARG   0.003   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02822 (  483)
  hydrogen bonds       : angle       4.05650 ( 1374)
  covalent geometry    : bond        0.00335 (12007)
  covalent geometry    : angle       0.56882 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 1.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8657 (pp)
REVERT: B  276 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6150 (pp20)
REVERT: C   37 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.5913 (p-80)
REVERT: C  133 MET cc_start: 0.8875 (mtm) cc_final: 0.8508 (ptp)
REVERT: C  295 MET cc_start: 0.9276 (mmp) cc_final: 0.8808 (mmm)
REVERT: E  138 MET cc_start: 0.8231 (tmm) cc_final: 0.7969 (tmm)
REVERT: E  147 MET cc_start: 0.8557 (mmm) cc_final: 0.8152 (mmt)
REVERT: E  186 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9024 (p)
REVERT: A   62 MET cc_start: 0.8298 (tpt) cc_final: 0.7872 (tpt)
REVERT: A  125 MET cc_start: 0.9055 (mpp) cc_final: 0.8343 (mpp)
REVERT: A  137 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8879 (m)
REVERT: A  209 MET cc_start: 0.8966 (mmm) cc_final: 0.8748 (mmm)
REVERT: A  231 MET cc_start: 0.8761 (mtt) cc_final: 0.8038 (mtt)
  outliers start: 28
  outliers final: 21
  residues processed: 79
  average time/residue: 0.1918
  time to fit residues: 24.8482
Evaluate side-chains
  78 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 6 optimal weight:    0.1980
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 93 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.048427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.037468 restraints weight = 60904.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.038781 restraints weight = 32532.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.039663 restraints weight = 21470.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12007  Z= 0.124
  Angle     :  0.559  11.025  16298  Z= 0.276
  Chirality :  0.042   0.232   1880
  Planarity :  0.003   0.030   2090
  Dihedral  :  4.317  28.802   1665
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.95 %
    Favored  : 79.22 %
  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: -0.46 (0.23), residues: 1515
  helix:  1.57 (0.21), residues: 678
  sheet: -1.94 (0.31), residues: 252
  loop : -1.81 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.003   0.001   HIS C  37 
 PHE   0.011   0.001   PHE E  64 
 TYR   0.016   0.001   TYR C  13 
 ARG   0.003   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02730 (  483)
  hydrogen bonds       : angle       3.95937 ( 1374)
  covalent geometry    : bond        0.00279 (12007)
  covalent geometry    : angle       0.55855 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 54
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7553 (m-10)
REVERT: B  201 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8641 (pp)
REVERT: B  276 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6531 (pp20)
REVERT: C   37 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.5976 (p-80)
REVERT: C   79 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8714 (tt)
REVERT: C  133 MET cc_start: 0.8858 (mtm) cc_final: 0.8493 (ptp)
REVERT: C  272 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8683 (mm)
REVERT: C  295 MET cc_start: 0.9252 (mmp) cc_final: 0.8749 (mmm)
REVERT: E   88 MET cc_start: 0.8649 (tpp) cc_final: 0.8330 (tpp)
REVERT: E  138 MET cc_start: 0.8215 (tmm) cc_final: 0.7980 (tmm)
REVERT: E  147 MET cc_start: 0.8552 (mmm) cc_final: 0.8150 (mmt)
REVERT: E  186 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8982 (p)
REVERT: A   62 MET cc_start: 0.8279 (tpt) cc_final: 0.7990 (tpt)
REVERT: A  125 MET cc_start: 0.9073 (mpp) cc_final: 0.8361 (mpp)
REVERT: A  137 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8863 (m)
REVERT: A  231 MET cc_start: 0.8745 (mtt) cc_final: 0.8013 (mtt)
  outliers start: 35
  outliers final: 21
  residues processed: 86
  average time/residue: 0.1797
  time to fit residues: 25.3149
Evaluate side-chains
  80 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 51
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue   55 ILE
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 8 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 101 optimal weight:    9.9990
   chunk 91 optimal weight:    0.8980
   chunk 128 optimal weight:    9.9990
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.047916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.036902 restraints weight = 61363.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.038190 restraints weight = 33084.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.039066 restraints weight = 22001.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12007  Z= 0.162
  Angle     :  0.589  10.146  16298  Z= 0.290
  Chirality :  0.043   0.235   1880
  Planarity :  0.003   0.031   2090
  Dihedral  :  4.382  28.592   1665
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.51 %
    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: -0.48 (0.22), residues: 1515
  helix:  1.61 (0.21), residues: 674
  sheet: -1.99 (0.31), residues: 255
  loop : -1.85 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 240 
 HIS   0.003   0.001   HIS C  37 
 PHE   0.011   0.001   PHE E  64 
 TYR   0.018   0.001   TYR B 291 
 ARG   0.003   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02833 (  483)
  hydrogen bonds       : angle       4.06847 ( 1374)
  covalent geometry    : bond        0.00360 (12007)
  covalent geometry    : angle       0.58947 (16298)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 51
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8641 (pp)
REVERT: C   37 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.5995 (p-80)
REVERT: C   79 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8707 (tt)
REVERT: C  133 MET cc_start: 0.8861 (mtm) cc_final: 0.8439 (ptp)
REVERT: C  272 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8737 (mm)
REVERT: C  295 MET cc_start: 0.9297 (mmp) cc_final: 0.8817 (mmm)
REVERT: E   88 MET cc_start: 0.8640 (tpp) cc_final: 0.8320 (tpp)
REVERT: E  138 MET cc_start: 0.8190 (tmm) cc_final: 0.7970 (tmm)
REVERT: E  147 MET cc_start: 0.8564 (mmm) cc_final: 0.8151 (mmt)
REVERT: E  186 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9006 (p)
REVERT: A   62 MET cc_start: 0.8297 (tpt) cc_final: 0.7996 (tpt)
REVERT: A  125 MET cc_start: 0.9089 (mpp) cc_final: 0.8375 (mpp)
REVERT: A  231 MET cc_start: 0.9220 (mtt) cc_final: 0.8808 (mtt)
  outliers start: 27
  outliers final: 20
  residues processed: 75
  average time/residue: 0.1807
  time to fit residues: 22.1763
Evaluate side-chains
  76 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 51
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  336 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 123 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 147 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 142 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.047501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.036559 restraints weight = 61475.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.037841 restraints weight = 33148.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.038719 restraints weight = 21983.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12007  Z= 0.181
  Angle     :  0.610  10.465  16298  Z= 0.299
  Chirality :  0.043   0.234   1880
  Planarity :  0.003   0.030   2090
  Dihedral  :  4.452  28.110   1665
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.43 %
    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: -0.49 (0.22), residues: 1515
  helix:  1.60 (0.21), residues: 676
  sheet: -2.04 (0.30), residues: 255
  loop : -1.83 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 240 
 HIS   0.003   0.001   HIS C 194 
 PHE   0.011   0.001   PHE D 157 
 TYR   0.018   0.001   TYR B 291 
 ARG   0.004   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02919 (  483)
  hydrogen bonds       : angle       4.13511 ( 1374)
  covalent geometry    : bond        0.00401 (12007)
  covalent geometry    : angle       0.61006 (16298)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2984.71 seconds
wall clock time: 53 minutes 11.24 seconds (3191.24 seconds total)