Starting phenix.real_space_refine
on Wed Mar  4 07:26:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o14_12689/03_2026/7o14_12689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o14_12689/03_2026/7o14_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_12689/03_2026/7o14_12689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o14_12689/03_2026/7o14_12689.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o14_12689/03_2026/7o14_12689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o14_12689/03_2026/7o14_12689.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.81, per 1000 atoms: 0.24
  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: 0.86
  Conformation dependent library (CDL) restraints added in 541.3 milliseconds
  

  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: 0.36
  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: 1.82

  Time building geometry restraints manager: 1.19 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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     11.720
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.040
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.023   0.002   ARG C 233 
 TYR   0.018   0.003   TYR A 204 
 PHE   0.019   0.003   PHE A  56 
 TRP   0.018   0.002   TRP E 155 
 HIS   0.012   0.002   HIS C 194 

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

*********************** 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  : 0.534 
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: 0.1299
  time to fit residues: 18.9254
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  : 0.529 
-------------------------------------------------------------------------------
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 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    0.0980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 225 ASN
E 108 HIS
E 225 ASN
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: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.049510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.038483 restraints weight = 59441.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.039879 restraints weight = 30372.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.040823 restraints weight = 19514.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.041461 restraints weight = 14335.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.041884 restraints weight = 11556.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12007  Z= 0.110
  Angle     :  0.594   9.401  16298  Z= 0.310
  Chirality :  0.043   0.176   1880
  Planarity :  0.005   0.041   2090
  Dihedral  :  5.146  33.694   1665
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.69 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.65 (0.18), residues: 1515
  helix: -2.04 (0.16), residues: 670
  sheet: -2.78 (0.31), residues: 204
  loop : -2.57 (0.21), residues: 641

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (12007)
  covalent geometry    : angle       0.59356 (16298)
  hydrogen bonds       : bond        0.03827 (  483)
  hydrogen bonds       : angle       5.09593 ( 1374)

*********************** 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
  86 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  304 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8950 (mm-40)
REVERT: E  138 MET cc_start: 0.8272 (tmm) cc_final: 0.7947 (tmm)
REVERT: E  213 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9107 (mt)
REVERT: A  209 MET cc_start: 0.8851 (mmm) cc_final: 0.8594 (mmm)
REVERT: A  231 MET cc_start: 0.8769 (mtt) cc_final: 0.7968 (mtt)
REVERT: A  305 LYS cc_start: 0.9303 (mmtt) cc_final: 0.8536 (mmmm)
  outliers start: 18
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1129
  time to fit residues: 13.9398
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  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 E residue  213 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  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 139 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 123 optimal weight:   10.0000
   chunk 133 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 120 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 112 optimal weight:   20.0000
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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
D 205 ASN
A  30 GLN
A  63 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.047745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.036855 restraints weight = 61547.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.038149 restraints weight = 32588.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.039045 restraints weight = 21324.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.039646 restraints weight = 15875.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.040056 restraints weight = 12904.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12007  Z= 0.208
  Angle     :  0.630   8.664  16298  Z= 0.322
  Chirality :  0.043   0.181   1880
  Planarity :  0.004   0.035   2090
  Dihedral  :  4.899  32.272   1665
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.20 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.20), residues: 1515
  helix: -0.41 (0.19), residues: 669
  sheet: -2.62 (0.29), residues: 231
  loop : -2.31 (0.23), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 233 
 TYR   0.016   0.002   TYR B 291 
 PHE   0.013   0.001   PHE D 120 
 TRP   0.008   0.001   TRP E 259 
 HIS   0.003   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (12007)
  covalent geometry    : angle       0.62975 (16298)
  hydrogen bonds       : bond        0.03533 (  483)
  hydrogen bonds       : angle       4.62475 ( 1374)

*********************** 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
  75 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  133 MET cc_start: 0.8847 (mtm) cc_final: 0.8585 (mtm)
REVERT: E  138 MET cc_start: 0.8209 (tmm) cc_final: 0.7831 (tmm)
REVERT: A  125 MET cc_start: 0.9047 (mpp) cc_final: 0.8395 (mpp)
REVERT: A  137 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.9015 (m)
REVERT: A  305 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8530 (mmmm)
  outliers start: 21
  outliers final: 13
  residues processed: 73
  average time/residue: 0.0944
  time to fit residues: 10.8323
Evaluate side-chains
  64 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  286 LYS
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 124 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 102 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 132 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0050
   chunk 31 optimal weight:    9.9990
   overall best weight:    3.1400

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.048402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.037545 restraints weight = 62614.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.038828 restraints weight = 33621.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.039704 restraints weight = 22186.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.040295 restraints weight = 16576.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.040703 restraints weight = 13545.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12007  Z= 0.191
  Angle     :  0.595   8.326  16298  Z= 0.303
  Chirality :  0.043   0.181   1880
  Planarity :  0.003   0.031   2090
  Dihedral  :  4.750  31.113   1665
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.09 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.21), residues: 1515
  helix:  0.36 (0.20), residues: 676
  sheet: -2.52 (0.29), residues: 241
  loop : -2.17 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 233 
 TYR   0.013   0.001   TYR B 291 
 PHE   0.012   0.001   PHE E 157 
 TRP   0.006   0.001   TRP E 259 
 HIS   0.004   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (12007)
  covalent geometry    : angle       0.59501 (16298)
  hydrogen bonds       : bond        0.03191 (  483)
  hydrogen bonds       : angle       4.41807 ( 1374)

*********************** 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
  86 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 54
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8664 (pp)
REVERT: C  133 MET cc_start: 0.8928 (mtm) cc_final: 0.8591 (mtm)
REVERT: E   83 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8260 (mm-30)
REVERT: E  138 MET cc_start: 0.8152 (tmm) cc_final: 0.7806 (tmm)
REVERT: A  125 MET cc_start: 0.9035 (mpp) cc_final: 0.8219 (mpp)
REVERT: A  209 MET cc_start: 0.9019 (mmm) cc_final: 0.8752 (mmm)
REVERT: A  231 MET cc_start: 0.8574 (mtt) cc_final: 0.7530 (mtt)
  outliers start: 32
  outliers final: 21
  residues processed: 82
  average time/residue: 0.0875
  time to fit residues: 11.3869
Evaluate side-chains
  73 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 51
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
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  183 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   84 THR
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 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
Chi-restraints excluded: chain A residue  390 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 141 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 104 optimal weight:    8.9990
   chunk 108 optimal weight:    0.6980
   chunk 133 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
C 214 GLN
** 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 = 0.3009 r_free = 0.3009 target = 0.046356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.035680 restraints weight = 62334.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.036923 restraints weight = 33023.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.037785 restraints weight = 21687.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.038373 restraints weight = 16200.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.038737 restraints weight = 13184.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  12007  Z= 0.287
  Angle     :  0.700   9.171  16298  Z= 0.347
  Chirality :  0.045   0.180   1880
  Planarity :  0.004   0.033   2090
  Dihedral  :  4.911  29.235   1665
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.30 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.22), residues: 1515
  helix:  0.63 (0.21), residues: 675
  sheet: -2.40 (0.29), residues: 265
  loop : -2.19 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 233 
 TYR   0.017   0.002   TYR B 291 
 PHE   0.015   0.002   PHE D 157 
 TRP   0.011   0.001   TRP A  45 
 HIS   0.005   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (12007)
  covalent geometry    : angle       0.69985 (16298)
  hydrogen bonds       : bond        0.03491 (  483)
  hydrogen bonds       : angle       4.64074 ( 1374)

*********************** 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
  85 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 48
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8639 (pp)
REVERT: C   37 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.5641 (p-80)
REVERT: C  133 MET cc_start: 0.9001 (mtm) cc_final: 0.8622 (mtm)
REVERT: C  295 MET cc_start: 0.9333 (mmm) cc_final: 0.9060 (mmm)
REVERT: E   83 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8330 (mm-30)
REVERT: E  138 MET cc_start: 0.8166 (tmm) cc_final: 0.7809 (tmm)
REVERT: E  186 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9023 (p)
REVERT: A  125 MET cc_start: 0.9034 (mpp) cc_final: 0.8290 (mpp)
REVERT: A  209 MET cc_start: 0.9163 (mmm) cc_final: 0.8824 (mmt)
REVERT: A  231 MET cc_start: 0.8587 (mtt) cc_final: 0.7828 (mtt)
  outliers start: 37
  outliers final: 21
  residues processed: 82
  average time/residue: 0.0867
  time to fit residues: 11.5610
Evaluate side-chains
  70 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  258 VAL
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain D residue   24 ILE
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  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 2 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 120 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3054 r_free = 0.3054 target = 0.047800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.036895 restraints weight = 61735.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.038194 restraints weight = 33030.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.039057 restraints weight = 21814.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.039675 restraints weight = 16366.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.040088 restraints weight = 13314.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2938

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= 0.126
  Angle     :  0.555   9.036  16298  Z= 0.280
  Chirality :  0.042   0.180   1880
  Planarity :  0.003   0.032   2090
  Dihedral  :  4.600  30.092   1665
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.95 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.22), residues: 1515
  helix:  1.06 (0.21), residues: 676
  sheet: -2.25 (0.30), residues: 255
  loop : -2.04 (0.24), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 233 
 TYR   0.015   0.001   TYR D 221 
 PHE   0.013   0.001   PHE E  64 
 TRP   0.008   0.001   TRP D 253 
 HIS   0.003   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12007)
  covalent geometry    : angle       0.55482 (16298)
  hydrogen bonds       : bond        0.02905 (  483)
  hydrogen bonds       : angle       4.14662 ( 1374)

*********************** 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
  84 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7513 (m-10)
REVERT: B  201 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8686 (pp)
REVERT: B  276 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5577 (pp20)
REVERT: C   37 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.5906 (p-80)
REVERT: C  272 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8725 (mm)
REVERT: C  295 MET cc_start: 0.9279 (mmm) cc_final: 0.9044 (mmm)
REVERT: D  201 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8980 (mm-30)
REVERT: E   88 MET cc_start: 0.8563 (tpp) cc_final: 0.8241 (tpp)
REVERT: E  138 MET cc_start: 0.8158 (tmm) cc_final: 0.7823 (tmm)
REVERT: E  186 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8918 (p)
REVERT: A   62 MET cc_start: 0.8300 (tpt) cc_final: 0.8007 (tpt)
REVERT: A  125 MET cc_start: 0.9055 (mpp) cc_final: 0.8220 (mpp)
REVERT: A  231 MET cc_start: 0.8646 (mtt) cc_final: 0.7989 (mtt)
  outliers start: 31
  outliers final: 20
  residues processed: 77
  average time/residue: 0.0824
  time to fit residues: 10.4962
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  : 0.461 
-------------------------------------------------------------------------------
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   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 D residue  247 VAL
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue   11 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  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  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 7 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 130 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 139 optimal weight:    6.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3059 r_free = 0.3059 target = 0.047965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.037020 restraints weight = 61019.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.038332 restraints weight = 32575.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.039204 restraints weight = 21476.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.039807 restraints weight = 16099.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.040220 restraints weight = 13137.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12007  Z= 0.129
  Angle     :  0.548   8.669  16298  Z= 0.275
  Chirality :  0.042   0.179   1880
  Planarity :  0.003   0.032   2090
  Dihedral  :  4.446  29.354   1665
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.19 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.22), residues: 1515
  helix:  1.32 (0.21), residues: 676
  sheet: -2.19 (0.30), residues: 255
  loop : -1.98 (0.24), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 233 
 TYR   0.016   0.001   TYR C  13 
 PHE   0.012   0.001   PHE E  64 
 TRP   0.007   0.001   TRP A  45 
 HIS   0.003   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (12007)
  covalent geometry    : angle       0.54821 (16298)
  hydrogen bonds       : bond        0.02800 (  483)
  hydrogen bonds       : angle       4.03028 ( 1374)

*********************** 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
  89 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 55
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7517 (m-10)
REVERT: B  201 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8597 (pp)
REVERT: B  276 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.5738 (pp20)
REVERT: C   37 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.5972 (p-80)
REVERT: C  272 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8727 (mm)
REVERT: D  201 GLU cc_start: 0.9227 (mt-10) cc_final: 0.9017 (mm-30)
REVERT: E   88 MET cc_start: 0.8615 (tpp) cc_final: 0.8307 (tpp)
REVERT: E  138 MET cc_start: 0.8176 (tmm) cc_final: 0.7856 (tmm)
REVERT: E  186 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8897 (p)
REVERT: A   62 MET cc_start: 0.8381 (tpt) cc_final: 0.8082 (tpt)
REVERT: A   81 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9157 (mm)
REVERT: A  125 MET cc_start: 0.9068 (mpp) cc_final: 0.8353 (mpp)
REVERT: A  137 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8920 (m)
REVERT: A  231 MET cc_start: 0.8636 (mtt) cc_final: 0.7988 (mtt)
REVERT: A  305 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8521 (mmmt)
REVERT: A  390 MET cc_start: 0.8071 (mmm) cc_final: 0.7740 (mmm)
  outliers start: 34
  outliers final: 21
  residues processed: 85
  average time/residue: 0.0817
  time to fit residues: 11.2659
Evaluate side-chains
  81 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 52
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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 B residue  280 ILE
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 C residue  139 LEU
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   92 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 135 optimal weight:   40.0000
   chunk 46 optimal weight:    0.9990
   chunk 112 optimal weight:   30.0000
   chunk 14 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3047 r_free = 0.3047 target = 0.047567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.036634 restraints weight = 61583.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.037918 restraints weight = 33021.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.038789 restraints weight = 21852.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.039384 restraints weight = 16385.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.039799 restraints weight = 13402.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.3106

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= 0.164
  Angle     :  0.569   8.497  16298  Z= 0.286
  Chirality :  0.042   0.177   1880
  Planarity :  0.003   0.032   2090
  Dihedral  :  4.471  28.739   1665
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.11 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.22), residues: 1515
  helix:  1.37 (0.21), residues: 676
  sheet: -2.16 (0.30), residues: 255
  loop : -1.96 (0.24), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 233 
 TYR   0.016   0.001   TYR C  13 
 PHE   0.012   0.001   PHE D 157 
 TRP   0.013   0.001   TRP C 240 
 HIS   0.003   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12007)
  covalent geometry    : angle       0.56903 (16298)
  hydrogen bonds       : bond        0.02950 (  483)
  hydrogen bonds       : angle       4.11828 ( 1374)

*********************** 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
  88 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 50
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8616 (pp)
REVERT: B  276 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.5819 (pp20)
REVERT: C   37 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.5872 (p-80)
REVERT: C   79 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8707 (tt)
REVERT: C  133 MET cc_start: 0.9173 (mmm) cc_final: 0.8967 (mmm)
REVERT: C  272 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8821 (mm)
REVERT: D  146 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8208 (t80)
REVERT: E   88 MET cc_start: 0.8660 (tpp) cc_final: 0.8344 (tpp)
REVERT: E  138 MET cc_start: 0.8185 (tmm) cc_final: 0.7878 (tmm)
REVERT: E  186 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8921 (p)
REVERT: A   62 MET cc_start: 0.8368 (tpt) cc_final: 0.8015 (tpt)
REVERT: A  125 MET cc_start: 0.9084 (mpp) cc_final: 0.8354 (mpp)
REVERT: A  231 MET cc_start: 0.8661 (mtt) cc_final: 0.7670 (mtt)
REVERT: A  305 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8518 (mmmt)
REVERT: A  390 MET cc_start: 0.8080 (mmm) cc_final: 0.7716 (mmm)
  outliers start: 38
  outliers final: 24
  residues processed: 83
  average time/residue: 0.0818
  time to fit residues: 11.2158
Evaluate side-chains
  81 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 50
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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 B residue  276 GLU
Chi-restraints excluded: chain B residue  280 ILE
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 D residue  146 PHE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue   11 GLU
Chi-restraints excluded: chain E residue   69 ILE
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  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  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 34 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 136 optimal weight:    4.9990
   chunk 128 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 118 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 95 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.047272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.036383 restraints weight = 61209.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.037652 restraints weight = 32860.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.038520 restraints weight = 21719.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.039112 restraints weight = 16328.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.039518 restraints weight = 13329.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.3172

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= 0.190
  Angle     :  0.601   9.599  16298  Z= 0.299
  Chirality :  0.043   0.177   1880
  Planarity :  0.003   0.032   2090
  Dihedral  :  4.529  28.242   1665
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.19 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.22), residues: 1515
  helix:  1.44 (0.21), residues: 671
  sheet: -2.17 (0.30), residues: 257
  loop : -1.89 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 233 
 TYR   0.020   0.002   TYR D 221 
 PHE   0.012   0.001   PHE D 157 
 TRP   0.008   0.001   TRP A  45 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (12007)
  covalent geometry    : angle       0.60098 (16298)
  hydrogen bonds       : bond        0.03010 (  483)
  hydrogen bonds       : angle       4.21174 ( 1374)

*********************** 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
  84 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 48
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8593 (pp)
REVERT: B  276 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.5849 (pp20)
REVERT: C   37 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.5900 (p-80)
REVERT: C   79 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8730 (tt)
REVERT: C  272 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8835 (mm)
REVERT: D  146 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8253 (t80)
REVERT: E  138 MET cc_start: 0.8156 (tmm) cc_final: 0.7861 (tmm)
REVERT: E  147 MET cc_start: 0.8554 (mmm) cc_final: 0.8096 (mmt)
REVERT: E  186 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8931 (p)
REVERT: A   62 MET cc_start: 0.8283 (tpt) cc_final: 0.7870 (tpt)
REVERT: A  125 MET cc_start: 0.9099 (mpp) cc_final: 0.8353 (mpp)
REVERT: A  231 MET cc_start: 0.8992 (mtt) cc_final: 0.8338 (mtt)
REVERT: A  390 MET cc_start: 0.8088 (mmm) cc_final: 0.7702 (mmm)
  outliers start: 36
  outliers final: 25
  residues processed: 81
  average time/residue: 0.0936
  time to fit residues: 12.5159
Evaluate side-chains
  80 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 48
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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 B residue  276 GLU
Chi-restraints excluded: chain B residue  280 ILE
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 D residue  146 PHE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain E residue    7 ILE
Chi-restraints excluded: chain E residue   11 GLU
Chi-restraints excluded: chain E residue   69 ILE
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  186 VAL
Chi-restraints excluded: chain E residue  259 TRP
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  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 21 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0050
   chunk 54 optimal weight:    8.9990
   chunk 121 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 94 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0970
   chunk 4 optimal weight:    1.9990
   chunk 117 optimal weight:   20.0000
   chunk 59 optimal weight:    5.9990
   overall best weight:    1.3796

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3073 r_free = 0.3073 target = 0.048454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.037545 restraints weight = 60858.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.038864 restraints weight = 32416.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.039749 restraints weight = 21327.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.040378 restraints weight = 15944.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.040799 restraints weight = 12967.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12007  Z= 0.110
  Angle     :  0.552  10.450  16298  Z= 0.274
  Chirality :  0.042   0.178   1880
  Planarity :  0.003   0.032   2090
  Dihedral  :  4.355  28.775   1665
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.76 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.23), residues: 1515
  helix:  1.64 (0.21), residues: 673
  sheet: -2.04 (0.31), residues: 252
  loop : -1.79 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 222 
 TYR   0.018   0.001   TYR D 221 
 PHE   0.010   0.001   PHE E  64 
 TRP   0.009   0.001   TRP C 240 
 HIS   0.003   0.001   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (12007)
  covalent geometry    : angle       0.55198 (16298)
  hydrogen bonds       : bond        0.02727 (  483)
  hydrogen bonds       : angle       3.93770 ( 1374)

********************** 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
  79 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 50
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8555 (pp)
REVERT: B  276 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6046 (pp20)
REVERT: C   37 HIS cc_start: 0.7189 (OUTLIER) cc_final: 0.5847 (p-80)
REVERT: C  272 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: E   88 MET cc_start: 0.8684 (tpp) cc_final: 0.8407 (tpp)
REVERT: E  138 MET cc_start: 0.8264 (tmm) cc_final: 0.7982 (tmm)
REVERT: E  147 MET cc_start: 0.8493 (mmm) cc_final: 0.8043 (mmt)
REVERT: E  186 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.9029 (p)
REVERT: A   62 MET cc_start: 0.8330 (tpt) cc_final: 0.8072 (tpt)
REVERT: A   81 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9136 (mm)
REVERT: A  125 MET cc_start: 0.9121 (mpp) cc_final: 0.8364 (mpp)
REVERT: A  231 MET cc_start: 0.9074 (mtt) cc_final: 0.8518 (mtt)
REVERT: A  390 MET cc_start: 0.8075 (mmm) cc_final: 0.7766 (mmm)
  outliers start: 29
  outliers final: 19
  residues processed: 77
  average time/residue: 0.0842
  time to fit residues: 10.6585
Evaluate side-chains
  74 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 49
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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  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 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   11 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  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  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 142 optimal weight:    8.9990
   chunk 141 optimal weight:    4.9990
   chunk 122 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 137 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 135 optimal weight:    0.0040
   chunk 22 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    2.6000

-------------------------------------------------------------------------------
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 = 0.3052 r_free = 0.3052 target = 0.047724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.036753 restraints weight = 61756.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.038039 restraints weight = 33266.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.038909 restraints weight = 22074.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.039522 restraints weight = 16623.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.039935 restraints weight = 13572.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.3282

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= 0.162
  Angle     :  0.580  10.412  16298  Z= 0.288
  Chirality :  0.042   0.177   1880
  Planarity :  0.003   0.031   2090
  Dihedral  :  4.407  28.223   1665
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.67 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.22), residues: 1515
  helix:  1.64 (0.21), residues: 673
  sheet: -2.07 (0.30), residues: 255
  loop : -1.81 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 233 
 TYR   0.018   0.001   TYR D 221 
 PHE   0.011   0.001   PHE D 157 
 TRP   0.009   0.001   TRP E 259 
 HIS   0.003   0.001   HIS C 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (12007)
  covalent geometry    : angle       0.57999 (16298)
  hydrogen bonds       : bond        0.02884 (  483)
  hydrogen bonds       : angle       4.05194 ( 1374)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1553.13 seconds
wall clock time: 27 minutes 51.38 seconds (1671.38 seconds total)