Starting phenix.real_space_refine
on Tue Jul 29 22:12:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o10_12685/07_2025/7o10_12685.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o10_12685/07_2025/7o10_12685.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o10_12685/07_2025/7o10_12685.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o10_12685/07_2025/7o10_12685.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o10_12685/07_2025/7o10_12685.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o10_12685/07_2025/7o10_12685.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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      37      5.16       5
     C    7466      2.51       5
     N    2038      2.21       5
     O    2109      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11651
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: "B"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2303
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 12, 'TRANS': 286}
    Chain: "C"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2295
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 12, 'TRANS': 285}
    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: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 7.78, per 1000 atoms: 0.67
  Number of scatterers: 11651
  At special positions: 0
  Unit cell: (86.184, 168.264, 138.51, 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      37     16.00
     Mg      1     11.99
     O    2109      8.00
     N    2038      7.00
     C    7466      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: 2.63
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2722

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 12 sheets defined
      47.1% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 344 through 348
      removed outlier: 4.243A  pdb=" N   GLY A 347 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.560A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   TRP A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
    Processing helix  chain 'A' and resid 392 through 405
      removed outlier: 3.559A  pdb=" N   GLN A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 50
      removed outlier: 3.907A  pdb=" N   SER B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS B  47 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU B  50 " --> pdb=" O   MET B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
    Processing helix  chain 'B' and resid 69 through 74
      removed outlier: 3.532A  pdb=" N   ARG B  74 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 102
    Processing helix  chain 'B' and resid 106 through 116
      removed outlier: 4.589A  pdb=" N   ASP B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.572A  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 177
      removed outlier: 3.601A  pdb=" N   GLN B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP B 166 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG B 177 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 192
      removed outlier: 4.293A  pdb=" N   VAL B 191 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLU B 192 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 187 through 192'
    Processing helix  chain 'B' and resid 211 through 219
    Processing helix  chain 'B' and resid 264 through 270
    Processing helix  chain 'B' and resid 270 through 275
      removed outlier: 3.843A  pdb=" N   GLU B 274 " --> pdb=" O   GLN B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.718A  pdb=" N   GLU B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 51
      removed outlier: 4.015A  pdb=" N   SER C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 74
      removed outlier: 3.723A  pdb=" N   ARG C  73 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG C  74 " --> pdb=" O   PRO C  70 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 69 through 74'
    Processing helix  chain 'C' and resid 90 through 103
      removed outlier: 3.684A  pdb=" N   THR C  94 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 114
      removed outlier: 3.894A  pdb=" N   GLU C 111 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
      removed outlier: 3.531A  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
    Processing helix  chain 'C' and resid 160 through 177
      removed outlier: 3.566A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 4.164A  pdb=" N   ALA C 193 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 219
    Processing helix  chain 'C' and resid 233 through 241
      removed outlier: 3.510A  pdb=" N   ARG C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
      removed outlier: 3.574A  pdb=" N   LEU C 268 " --> pdb=" O   LYS C 264 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ARG C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLN C 270 " --> pdb=" O   VAL C 266 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU C 271 " --> pdb=" O   LEU C 267 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY C 273 " --> pdb=" O   ARG C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 298
      removed outlier: 3.542A  pdb=" N   LEU C 290 " --> pdb=" O   SER C 286 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 15
      removed outlier: 3.588A  pdb=" N   ILE D   7 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.516A  pdb=" N   ILE D  24 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.513A  pdb=" N   ILE D  55 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU D  58 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.540A  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: 3.731A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 4.113A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 146
    Processing helix  chain 'D' and resid 146 through 167
      removed outlier: 3.584A  pdb=" N   THR D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.596A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 201
      removed outlier: 3.548A  pdb=" N   SER D 200 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 215
    Processing helix  chain 'D' and resid 216 through 226
      removed outlier: 3.546A  pdb=" N   ASN D 225 " --> pdb=" O   TYR D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 244
      removed outlier: 3.764A  pdb=" N   LEU D 241 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.696A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
      removed outlier: 3.651A  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: 3.560A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.515A  pdb=" N   ILE E  24 " --> pdb=" O   TRP E  20 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.530A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET E  66 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
      removed outlier: 3.534A  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
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.808A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 124 through 129
    Processing helix  chain 'E' and resid 135 through 143
      removed outlier: 3.827A  pdb=" N   LEU E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   TRP E 141 " --> pdb=" O   GLY E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.792A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'E' and resid 211 through 215
    Processing helix  chain 'E' and resid 216 through 224
      removed outlier: 3.725A  pdb=" N   ILE E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 4.066A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40
      removed outlier: 8.081A  pdb=" N   ARG A  44 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   TRP A  45 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53
      removed outlier: 3.637A  pdb=" N   GLN A  73 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ILE A 199 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A 266 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.517A  pdb=" N   GLY A 131 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ILE A 251 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   TYR A 291 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   MET A 253 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLN A 332 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91
      removed outlier: 6.578A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL A 142 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217
      removed outlier: 7.577A  pdb=" N   SER A 322 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE A 298 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 11
      removed outlier: 5.740A  pdb=" N   VAL B   9 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.626A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ASP B 153 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LEU B  79 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU B 150 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU B 152 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 248
      removed outlier: 3.535A  pdb=" N   ALA B 259 " --> pdb=" O   VAL B 223 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG B 224 " --> pdb=" O   HIS B 283 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 24
      removed outlier: 5.592A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLN C  59 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79
      removed outlier: 6.931A  pdb=" N   LEU C 150 " --> pdb=" O   ILE C 182 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   CYS C 184 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU C 152 " --> pdb=" O   CYS C 184 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA C 198 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   VAL C 209 " --> pdb=" O   ALA C 198 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   ILE C 200 " --> pdb=" O   GLN C 207 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 254 through 255
      removed outlier: 3.590A  pdb=" N   ILE C 255 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 255
      removed outlier: 3.590A  pdb=" N   ILE C 255 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1359 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: 3.45

  Time building geometry restraints manager: 3.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3678
        1.34 -     1.46: 1830
        1.46 -     1.57: 6297
        1.57 -     1.69: 2
        1.69 -     1.81: 64
  Bond restraints: 11871
  Sorted by residual:
  bond pdb=" CA  ILE E  51 "
       pdb=" C   ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.525  1.597 -0.072 2.10e-02 2.27e+03 1.16e+01
  bond pdb=" CB  THR E 218 "
       pdb=" CG2 THR E 218 "
    ideal  model  delta    sigma   weight residual
    1.521  1.440  0.081 3.30e-02 9.18e+02 6.07e+00
  bond pdb=" CA  ILE E  51 "
       pdb=" CB  ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.540  1.600 -0.060 2.70e-02 1.37e+03 4.98e+00
  bond pdb=" C   LEU C 188 "
       pdb=" N   PRO C 189 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.77e+00
  bond pdb=" C   ILE E  51 "
       pdb=" N   PRO E  52 "
    ideal  model  delta    sigma   weight residual
    1.336  1.362 -0.026 1.25e-02 6.40e+03 4.35e+00
  ... (remaining 11866 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.65: 15854
        3.65 -     7.30: 229
        7.30 -    10.95: 29
       10.95 -    14.61: 2
       14.61 -    18.26: 2
  Bond angle restraints: 16116
  Sorted by residual:
  angle pdb=" CA  LEU A  35 "
        pdb=" CB  LEU A  35 "
        pdb=" CG  LEU A  35 "
      ideal   model   delta    sigma   weight residual
     116.30  134.56  -18.26 3.50e+00 8.16e-02 2.72e+01
  angle pdb=" CA  THR A 188 "
        pdb=" CB  THR A 188 "
        pdb=" CG2 THR A 188 "
      ideal   model   delta    sigma   weight residual
     110.50  119.05   -8.55 1.70e+00 3.46e-01 2.53e+01
  angle pdb=" C   GLN A 247 "
        pdb=" N   ASN A 248 "
        pdb=" CA  ASN A 248 "
      ideal   model   delta    sigma   weight residual
     121.54  130.57   -9.03 1.91e+00 2.74e-01 2.24e+01
  angle pdb=" CA  LEU E 112 "
        pdb=" CB  LEU E 112 "
        pdb=" CG  LEU E 112 "
      ideal   model   delta    sigma   weight residual
     116.30  132.30  -16.00 3.50e+00 8.16e-02 2.09e+01
  angle pdb=" C   ARG A 181 "
        pdb=" N   ASP A 182 "
        pdb=" CA  ASP A 182 "
      ideal   model   delta    sigma   weight residual
     121.54  130.21   -8.67 1.91e+00 2.74e-01 2.06e+01
  ... (remaining 16111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 6161
       16.82 -    33.63: 678
       33.63 -    50.45: 160
       50.45 -    67.26: 15
       67.26 -    84.07: 7
  Dihedral angle restraints: 7021
    sinusoidal: 2752
      harmonic: 4269
  Sorted by residual:
  dihedral pdb=" CA  VAL C  83 "
           pdb=" C   VAL C  83 "
           pdb=" N   THR C  84 "
           pdb=" CA  THR C  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.81   26.19     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  TRP C 240 "
           pdb=" C   TRP C 240 "
           pdb=" N   THR C 241 "
           pdb=" CA  THR C 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.56   23.44     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  LEU D  73 "
           pdb=" C   LEU D  73 "
           pdb=" N   ALA D  74 "
           pdb=" CA  ALA D  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.42  -22.58     0      5.00e+00 4.00e-02 2.04e+01
  ... (remaining 7018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1690
       0.103 -    0.205: 149
       0.205 -    0.308: 17
       0.308 -    0.410: 2
       0.410 -    0.513: 3
  Chirality restraints: 1861
  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   -2.12   -0.51 2.00e-01 2.50e+01 6.57e+00
  chirality pdb=" CB  ILE B 230 "
            pdb=" CA  ILE B 230 "
            pdb=" CG1 ILE B 230 "
            pdb=" CG2 ILE B 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CB  VAL C 260 "
            pdb=" CA  VAL C 260 "
            pdb=" CG1 VAL C 260 "
            pdb=" CG2 VAL C 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.21   -0.42 2.00e-01 2.50e+01 4.33e+00
  ... (remaining 1858 not shown)

  Planarity restraints: 2063
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 376 "   -0.022 2.00e-02 2.50e+03   4.31e-02 1.86e+01
        pdb=" C   VAL A 376 "    0.075 2.00e-02 2.50e+03
        pdb=" O   VAL A 376 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ASP A 377 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  30 "   -0.017 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        pdb=" C   VAL D  30 "    0.057 2.00e-02 2.50e+03
        pdb=" O   VAL D  30 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU D  31 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 182 "    0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   ASP A 182 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASP A 182 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLY A 183 "    0.019 2.00e-02 2.50e+03
  ... (remaining 2060 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 102
        2.54 -     3.13: 7694
        3.13 -     3.72: 18541
        3.72 -     4.31: 26273
        4.31 -     4.90: 42946
  Nonbonded interactions: 95556
  Sorted by model distance:
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     1.946 2.170
  nonbonded pdb=" OD1 ASP A 359 "
            pdb="MG    MG A 501 "
     model   vdw
     2.018 2.170
  nonbonded pdb=" OD1 ASP A 363 "
            pdb="MG    MG A 501 "
     model   vdw
     2.184 2.170
  nonbonded pdb=" OD1 ASN A 361 "
            pdb="MG    MG A 501 "
     model   vdw
     2.292 2.170
  nonbonded pdb=" O   SER B  90 "
            pdb=" OG1 THR B  94 "
     model   vdw
     2.340 3.040
  ... (remaining 95551 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' and resid 2 through 299)
  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:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     28.830
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
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      :  0.006   0.083  11871  Z= 0.271
  Angle     :  1.086  18.258  16116  Z= 0.570
  Chirality :  0.065   0.513   1861
  Planarity :  0.007   0.075   2063
  Dihedral  : 14.559  84.075   4299
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.78 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.64 (0.15), residues: 1498
  helix: -4.51 (0.08), residues: 639
  sheet: -3.63 (0.26), residues: 215
  loop : -2.70 (0.21), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP C 240 
 HIS   0.009   0.002   HIS A 163 
 PHE   0.015   0.002   PHE E  64 
 TYR   0.017   0.002   TYR A  52 
 ARG   0.006   0.001   ARG A 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31494 (  483)
  hydrogen bonds       : angle      11.12987 ( 1359)
  covalent geometry    : bond        0.00589 (11871)
  covalent geometry    : angle       1.08588 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8903 (mpp) cc_final: 0.8479 (mpp)
REVERT: A  231 MET cc_start: 0.9149 (mtt) cc_final: 0.8858 (mtt)
REVERT: A  256 ILE cc_start: 0.9218 (pt) cc_final: 0.8941 (pt)
REVERT: A  420 MET cc_start: 0.8848 (mmm) cc_final: 0.8647 (mmm)
REVERT: B   61 LYS cc_start: 0.8778 (mttp) cc_final: 0.8436 (mmmt)
REVERT: C   86 TYR cc_start: 0.8963 (m-80) cc_final: 0.8665 (m-10)
REVERT: C  283 HIS cc_start: 0.7392 (m90) cc_final: 0.7021 (m90)
REVERT: C  287 LEU cc_start: 0.9380 (tp) cc_final: 0.8933 (tp)
REVERT: D   75 TYR cc_start: 0.9156 (p90) cc_final: 0.8909 (p90)
REVERT: D  139 LEU cc_start: 0.9176 (tp) cc_final: 0.8955 (tp)
REVERT: D  169 ASN cc_start: 0.8875 (p0) cc_final: 0.8326 (p0)
REVERT: D  219 ASP cc_start: 0.9034 (m-30) cc_final: 0.8745 (m-30)
REVERT: E    3 GLN cc_start: 0.8347 (mt0) cc_final: 0.8090 (mt0)
REVERT: E   82 ASP cc_start: 0.9165 (t0) cc_final: 0.8953 (t0)
REVERT: E  118 ILE cc_start: 0.8456 (mm) cc_final: 0.8175 (tt)
REVERT: E  171 LYS cc_start: 0.9232 (tttt) cc_final: 0.9016 (tttt)
REVERT: E  211 TRP cc_start: 0.8527 (m100) cc_final: 0.8162 (m-10)
REVERT: E  219 ASP cc_start: 0.8061 (m-30) cc_final: 0.7737 (m-30)
REVERT: E  221 TYR cc_start: 0.9022 (t80) cc_final: 0.8516 (t80)
  outliers start: 13
  outliers final: 7
  residues processed: 174
  average time/residue: 0.2866
  time to fit residues: 67.5118
Evaluate side-chains
  107 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue  112 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 122 ASN
A 123 ASN
A 141 GLN
A 145 ASN
A 160 ASN
A 175 ASN
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 417 HIS
B  11 GLN
B  20 HIS
B 176 GLN
B 207 GLN
B 283 HIS
C   2 ASN
C  75 GLN
C 135 GLN
C 214 GLN
C 283 HIS
D   6 ASN
D 205 ASN
D 225 ASN
E 108 HIS
E 225 ASN

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.064243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.051279 restraints weight = 46361.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.053088 restraints weight = 21419.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.054327 restraints weight = 13101.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11871  Z= 0.145
  Angle     :  0.619   8.544  16116  Z= 0.318
  Chirality :  0.043   0.268   1861
  Planarity :  0.005   0.044   2063
  Dihedral  :  5.280  24.684   1651
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.52 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.19), residues: 1498
  helix: -1.88 (0.16), residues: 655
  sheet: -3.18 (0.29), residues: 201
  loop : -2.24 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 240 
 HIS   0.004   0.001   HIS B 186 
 PHE   0.012   0.001   PHE D  64 
 TYR   0.016   0.001   TYR E 268 
 ARG   0.012   0.000   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  483)
  hydrogen bonds       : angle       4.99695 ( 1359)
  covalent geometry    : bond        0.00317 (11871)
  covalent geometry    : angle       0.61910 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8697 (mpp) cc_final: 0.8210 (mpp)
REVERT: A  231 MET cc_start: 0.9141 (mtt) cc_final: 0.8871 (mtp)
REVERT: A  233 SER cc_start: 0.9036 (m) cc_final: 0.8463 (t)
REVERT: A  297 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.7809 (p)
REVERT: A  400 TRP cc_start: 0.8531 (t60) cc_final: 0.8078 (t60)
REVERT: B   34 LEU cc_start: 0.9422 (tp) cc_final: 0.9210 (tp)
REVERT: B   61 LYS cc_start: 0.8819 (mttp) cc_final: 0.8520 (mmmt)
REVERT: B  295 MET cc_start: 0.9047 (mmm) cc_final: 0.8839 (mmm)
REVERT: C   78 TYR cc_start: 0.8677 (t80) cc_final: 0.8427 (t80)
REVERT: C  287 LEU cc_start: 0.9469 (tp) cc_final: 0.9025 (tp)
REVERT: D  117 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8722 (tt)
REVERT: D  171 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8773 (ttmm)
REVERT: D  219 ASP cc_start: 0.9065 (m-30) cc_final: 0.8716 (m-30)
REVERT: E    3 GLN cc_start: 0.8508 (mt0) cc_final: 0.8175 (mt0)
REVERT: E   20 TRP cc_start: 0.8485 (m100) cc_final: 0.7887 (m-10)
REVERT: E   82 ASP cc_start: 0.9156 (t0) cc_final: 0.8946 (t0)
REVERT: E  211 TRP cc_start: 0.8677 (m100) cc_final: 0.8436 (m-90)
REVERT: E  221 TYR cc_start: 0.9083 (t80) cc_final: 0.8837 (t80)
  outliers start: 26
  outliers final: 11
  residues processed: 142
  average time/residue: 0.2226
  time to fit residues: 46.6092
Evaluate side-chains
  112 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  203 LYS
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain E residue  100 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 132 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0370
   chunk 84 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 94 optimal weight:    9.9990
   overall best weight:    1.1662

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

Flipped N/Q/H residues before XYZ refinement:
A  30 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**
B 120 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.063753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.050735 restraints weight = 46708.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.052512 restraints weight = 21716.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.053708 restraints weight = 13365.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11871  Z= 0.136
  Angle     :  0.583  10.016  16116  Z= 0.293
  Chirality :  0.043   0.238   1861
  Planarity :  0.004   0.043   2063
  Dihedral  :  4.896  25.107   1646
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.99 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.21), residues: 1498
  helix: -0.36 (0.20), residues: 658
  sheet: -2.81 (0.30), residues: 208
  loop : -1.99 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 186 
 PHE   0.009   0.001   PHE E 157 
 TYR   0.014   0.001   TYR B  86 
 ARG   0.003   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  483)
  hydrogen bonds       : angle       4.39342 ( 1359)
  covalent geometry    : bond        0.00301 (11871)
  covalent geometry    : angle       0.58304 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8695 (mpp) cc_final: 0.8242 (mpp)
REVERT: A  390 MET cc_start: 0.8534 (tpp) cc_final: 0.8239 (tpp)
REVERT: A  400 TRP cc_start: 0.8365 (t60) cc_final: 0.8005 (t-100)
REVERT: A  420 MET cc_start: 0.8739 (mmm) cc_final: 0.8355 (tpp)
REVERT: B   34 LEU cc_start: 0.9437 (tp) cc_final: 0.9224 (tp)
REVERT: B   61 LYS cc_start: 0.8828 (mttp) cc_final: 0.8558 (mmmt)
REVERT: C   78 TYR cc_start: 0.8736 (t80) cc_final: 0.8412 (t80)
REVERT: C  287 LEU cc_start: 0.9443 (tp) cc_final: 0.8981 (tp)
REVERT: D  117 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8661 (tt)
REVERT: D  171 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8684 (ttmt)
REVERT: D  219 ASP cc_start: 0.8984 (m-30) cc_final: 0.8676 (m-30)
REVERT: E   20 TRP cc_start: 0.8537 (m100) cc_final: 0.7919 (m-10)
REVERT: E  211 TRP cc_start: 0.8691 (m100) cc_final: 0.8461 (m-90)
REVERT: E  219 ASP cc_start: 0.8641 (m-30) cc_final: 0.8077 (m-30)
REVERT: E  221 TYR cc_start: 0.9123 (t80) cc_final: 0.8863 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 129
  average time/residue: 0.2199
  time to fit residues: 42.5740
Evaluate side-chains
  117 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 127 optimal weight:    0.0870
   chunk 79 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 93 optimal weight:   20.0000
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.5562

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 270 GLN
C 245 HIS
E   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.062810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.050000 restraints weight = 47131.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.051749 restraints weight = 22006.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.052966 restraints weight = 13556.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11871  Z= 0.163
  Angle     :  0.588   9.511  16116  Z= 0.295
  Chirality :  0.043   0.247   1861
  Planarity :  0.004   0.040   2063
  Dihedral  :  4.785  28.092   1646
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.28 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.22), residues: 1498
  helix:  0.31 (0.21), residues: 675
  sheet: -2.55 (0.33), residues: 208
  loop : -1.90 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 186 
 PHE   0.011   0.001   PHE E 157 
 TYR   0.017   0.001   TYR E 268 
 ARG   0.003   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03129 (  483)
  hydrogen bonds       : angle       4.19116 ( 1359)
  covalent geometry    : bond        0.00363 (11871)
  covalent geometry    : angle       0.58849 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8733 (mpp) cc_final: 0.8253 (mpp)
REVERT: A  233 SER cc_start: 0.8868 (m) cc_final: 0.8175 (t)
REVERT: A  400 TRP cc_start: 0.8332 (t60) cc_final: 0.8003 (t-100)
REVERT: A  420 MET cc_start: 0.8779 (mmm) cc_final: 0.8363 (tpp)
REVERT: B   57 GLU cc_start: 0.7648 (tt0) cc_final: 0.7037 (tp30)
REVERT: B   61 LYS cc_start: 0.8829 (mttp) cc_final: 0.8585 (mmmt)
REVERT: B   86 TYR cc_start: 0.8854 (m-80) cc_final: 0.8542 (m-80)
REVERT: B  183 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9281 (mm)
REVERT: C   78 TYR cc_start: 0.8795 (t80) cc_final: 0.8552 (t80)
REVERT: D   63 THR cc_start: 0.9408 (m) cc_final: 0.9154 (m)
REVERT: D   82 ASP cc_start: 0.9042 (t0) cc_final: 0.8696 (t0)
REVERT: D  117 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8690 (tt)
REVERT: D  171 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8818 (ttmm)
REVERT: D  219 ASP cc_start: 0.8969 (m-30) cc_final: 0.8681 (m-30)
REVERT: E   10 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8815 (tttp)
REVERT: E   20 TRP cc_start: 0.8580 (m100) cc_final: 0.8071 (m-10)
REVERT: E  171 LYS cc_start: 0.9104 (tttt) cc_final: 0.8832 (tttm)
REVERT: E  211 TRP cc_start: 0.8730 (m100) cc_final: 0.8490 (m-90)
REVERT: E  219 ASP cc_start: 0.8577 (m-30) cc_final: 0.8007 (m-30)
REVERT: E  221 TYR cc_start: 0.9151 (t80) cc_final: 0.8950 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 131
  average time/residue: 0.2242
  time to fit residues: 43.5227
Evaluate side-chains
  122 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain E residue   10 LYS
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 128 optimal weight:    0.0470
   chunk 93 optimal weight:   20.0000
   chunk 124 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0370
   overall best weight:    1.0160

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.063353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.050641 restraints weight = 46489.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.052400 restraints weight = 21753.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.053621 restraints weight = 13416.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11871  Z= 0.123
  Angle     :  0.563  11.222  16116  Z= 0.278
  Chirality :  0.042   0.158   1861
  Planarity :  0.003   0.039   2063
  Dihedral  :  4.644  31.050   1646
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.12 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.22), residues: 1498
  helix:  0.66 (0.21), residues: 672
  sheet: -2.23 (0.35), residues: 189
  loop : -1.87 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.008   0.001   TYR B  86 
 ARG   0.003   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02894 (  483)
  hydrogen bonds       : angle       3.98148 ( 1359)
  covalent geometry    : bond        0.00277 (11871)
  covalent geometry    : angle       0.56332 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6931 (mmt) cc_final: 0.6706 (mmt)
REVERT: A  125 MET cc_start: 0.8748 (mpp) cc_final: 0.8237 (mpp)
REVERT: A  233 SER cc_start: 0.8983 (m) cc_final: 0.8172 (t)
REVERT: A  400 TRP cc_start: 0.8295 (t60) cc_final: 0.7968 (t-100)
REVERT: A  420 MET cc_start: 0.8804 (mmm) cc_final: 0.8398 (tpp)
REVERT: B   61 LYS cc_start: 0.8804 (mttp) cc_final: 0.8571 (mmmt)
REVERT: B   86 TYR cc_start: 0.8811 (m-80) cc_final: 0.8419 (m-80)
REVERT: B  183 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9318 (mm)
REVERT: B  271 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7741 (tp)
REVERT: C   78 TYR cc_start: 0.8877 (t80) cc_final: 0.8614 (t80)
REVERT: D   63 THR cc_start: 0.9405 (m) cc_final: 0.9138 (m)
REVERT: D  117 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8749 (tt)
REVERT: D  219 ASP cc_start: 0.8958 (m-30) cc_final: 0.8679 (m-30)
REVERT: D  268 TYR cc_start: 0.8876 (t80) cc_final: 0.8674 (t80)
REVERT: E   10 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8754 (tttp)
REVERT: E   20 TRP cc_start: 0.8597 (m100) cc_final: 0.8014 (m-10)
REVERT: E   76 ASP cc_start: 0.8738 (p0) cc_final: 0.8522 (p0)
REVERT: E   83 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8775 (mt-10)
REVERT: E  171 LYS cc_start: 0.9110 (tttt) cc_final: 0.8899 (tttm)
REVERT: E  219 ASP cc_start: 0.8557 (m-30) cc_final: 0.8034 (m-30)
  outliers start: 32
  outliers final: 18
  residues processed: 138
  average time/residue: 0.2129
  time to fit residues: 44.5826
Evaluate side-chains
  119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  203 LYS
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain E residue   10 LYS
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0060
   chunk 17 optimal weight:    3.9990
   chunk 129 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    2.2004

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** 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**
C  97 HIS
E   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.061295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.048745 restraints weight = 47713.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.050440 restraints weight = 22394.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.051589 restraints weight = 13847.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  11871  Z= 0.215
  Angle     :  0.641  10.439  16116  Z= 0.315
  Chirality :  0.044   0.182   1861
  Planarity :  0.004   0.038   2063
  Dihedral  :  4.826  40.698   1646
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.53 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.22), residues: 1498
  helix:  0.74 (0.21), residues: 671
  sheet: -1.99 (0.39), residues: 179
  loop : -1.84 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 240 
 HIS   0.005   0.001   HIS B 186 
 PHE   0.014   0.001   PHE E 157 
 TYR   0.018   0.001   TYR E 268 
 ARG   0.003   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  483)
  hydrogen bonds       : angle       4.12415 ( 1359)
  covalent geometry    : bond        0.00479 (11871)
  covalent geometry    : angle       0.64093 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 1.194 
Fit side-chains
REVERT: A  125 MET cc_start: 0.8822 (mpp) cc_final: 0.8280 (mpp)
REVERT: A  231 MET cc_start: 0.9159 (mtp) cc_final: 0.8943 (ptp)
REVERT: A  233 SER cc_start: 0.8762 (m) cc_final: 0.8053 (t)
REVERT: A  400 TRP cc_start: 0.8303 (t60) cc_final: 0.7989 (t-100)
REVERT: A  420 MET cc_start: 0.8841 (mmm) cc_final: 0.8501 (tpp)
REVERT: B   61 LYS cc_start: 0.8795 (mttp) cc_final: 0.8574 (mmmt)
REVERT: B  271 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7753 (tp)
REVERT: C   13 TYR cc_start: 0.8416 (p90) cc_final: 0.7309 (p90)
REVERT: C   16 MET cc_start: 0.8163 (mpp) cc_final: 0.7915 (mtm)
REVERT: D   63 THR cc_start: 0.9403 (m) cc_final: 0.9142 (m)
REVERT: D  117 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8779 (tt)
REVERT: D  187 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.8935 (pp)
REVERT: D  219 ASP cc_start: 0.8989 (m-30) cc_final: 0.8710 (m-30)
REVERT: E   20 TRP cc_start: 0.8581 (m100) cc_final: 0.8138 (m-10)
REVERT: E  219 ASP cc_start: 0.8639 (m-30) cc_final: 0.8328 (m-30)
  outliers start: 37
  outliers final: 21
  residues processed: 128
  average time/residue: 0.1922
  time to fit residues: 38.0050
Evaluate side-chains
  116 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   93 CYS
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:    0.1980
   chunk 109 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 112 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 119 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 143 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.063478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.050812 restraints weight = 46964.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.052587 restraints weight = 21542.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.053815 restraints weight = 13129.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11871  Z= 0.110
  Angle     :  0.577  10.602  16116  Z= 0.281
  Chirality :  0.042   0.174   1861
  Planarity :  0.003   0.038   2063
  Dihedral  :  4.576  39.379   1645
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.10 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.23), residues: 1498
  helix:  1.07 (0.21), residues: 666
  sheet: -1.80 (0.39), residues: 183
  loop : -1.76 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 
 PHE   0.011   0.001   PHE E 157 
 TYR   0.010   0.001   TYR C  13 
 ARG   0.002   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02799 (  483)
  hydrogen bonds       : angle       3.85981 ( 1359)
  covalent geometry    : bond        0.00254 (11871)
  covalent geometry    : angle       0.57694 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7241 (mmt) cc_final: 0.6842 (mmt)
REVERT: A  125 MET cc_start: 0.8828 (mpp) cc_final: 0.8237 (mpp)
REVERT: A  233 SER cc_start: 0.8956 (m) cc_final: 0.8219 (t)
REVERT: A  400 TRP cc_start: 0.8225 (t60) cc_final: 0.7909 (t-100)
REVERT: A  420 MET cc_start: 0.8819 (mmm) cc_final: 0.8492 (tpp)
REVERT: B   61 LYS cc_start: 0.8798 (mttp) cc_final: 0.8555 (mmmt)
REVERT: B  271 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7793 (tp)
REVERT: C   13 TYR cc_start: 0.8335 (p90) cc_final: 0.7189 (p90)
REVERT: C   16 MET cc_start: 0.8158 (mpp) cc_final: 0.7887 (mtt)
REVERT: C  224 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8508 (tmm-80)
REVERT: D   63 THR cc_start: 0.9392 (m) cc_final: 0.9102 (m)
REVERT: D  187 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8897 (pp)
REVERT: D  219 ASP cc_start: 0.9012 (m-30) cc_final: 0.8724 (m-30)
REVERT: E   20 TRP cc_start: 0.8546 (m100) cc_final: 0.7959 (m-10)
REVERT: E   76 ASP cc_start: 0.8703 (p0) cc_final: 0.8466 (p0)
REVERT: E   83 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8777 (mt-10)
REVERT: E  219 ASP cc_start: 0.8510 (m-30) cc_final: 0.8013 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 130
  average time/residue: 0.2236
  time to fit residues: 43.0651
Evaluate side-chains
  121 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 125 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0470
   chunk 113 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.9480

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.062116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.049630 restraints weight = 47081.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.051387 restraints weight = 21802.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.052577 restraints weight = 13363.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11871  Z= 0.122
  Angle     :  0.597  10.649  16116  Z= 0.290
  Chirality :  0.042   0.162   1861
  Planarity :  0.003   0.036   2063
  Dihedral  :  4.572  39.946   1645
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.42 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.23), residues: 1498
  helix:  1.15 (0.21), residues: 671
  sheet: -1.81 (0.39), residues: 178
  loop : -1.73 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 
 PHE   0.014   0.001   PHE A 110 
 TYR   0.022   0.001   TYR C  78 
 ARG   0.002   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02794 (  483)
  hydrogen bonds       : angle       3.81740 ( 1359)
  covalent geometry    : bond        0.00281 (11871)
  covalent geometry    : angle       0.59672 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8816 (mpp) cc_final: 0.8299 (mpp)
REVERT: A  233 SER cc_start: 0.8909 (m) cc_final: 0.8156 (t)
REVERT: A  400 TRP cc_start: 0.8231 (t60) cc_final: 0.7929 (t-100)
REVERT: A  420 MET cc_start: 0.8813 (mmm) cc_final: 0.8493 (tpp)
REVERT: B   61 LYS cc_start: 0.8783 (mttp) cc_final: 0.8554 (mmmt)
REVERT: B  271 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7719 (tp)
REVERT: C   13 TYR cc_start: 0.8327 (p90) cc_final: 0.8108 (p90)
REVERT: C   78 TYR cc_start: 0.8773 (t80) cc_final: 0.8305 (t80)
REVERT: C  224 ARG cc_start: 0.8896 (tmm-80) cc_final: 0.8648 (tmm-80)
REVERT: D   63 THR cc_start: 0.9410 (m) cc_final: 0.9124 (m)
REVERT: D  187 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8897 (pp)
REVERT: D  219 ASP cc_start: 0.9024 (m-30) cc_final: 0.8618 (m-30)
REVERT: E   20 TRP cc_start: 0.8558 (m100) cc_final: 0.8019 (m-10)
REVERT: E   83 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8773 (mt-10)
REVERT: E  219 ASP cc_start: 0.8533 (m-30) cc_final: 0.8010 (m-30)
REVERT: E  221 TYR cc_start: 0.9135 (t80) cc_final: 0.8903 (t80)
  outliers start: 34
  outliers final: 23
  residues processed: 127
  average time/residue: 0.2187
  time to fit residues: 41.9623
Evaluate side-chains
  125 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 144 optimal weight:    0.4980
   chunk 84 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** 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 = 0.3248 r_free = 0.3248 target = 0.060439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.047858 restraints weight = 48077.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.049591 restraints weight = 22177.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.050765 restraints weight = 13591.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11871  Z= 0.203
  Angle     :  0.657  10.100  16116  Z= 0.321
  Chirality :  0.044   0.161   1861
  Planarity :  0.003   0.037   2063
  Dihedral  :  4.789  42.418   1645
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.59 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.23), residues: 1498
  helix:  1.04 (0.21), residues: 675
  sheet: -1.69 (0.39), residues: 189
  loop : -1.68 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  45 
 HIS   0.004   0.001   HIS B 186 
 PHE   0.015   0.001   PHE A 110 
 TYR   0.021   0.002   TYR C  78 
 ARG   0.002   0.000   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  483)
  hydrogen bonds       : angle       4.01340 ( 1359)
  covalent geometry    : bond        0.00455 (11871)
  covalent geometry    : angle       0.65746 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 1.321 
Fit side-chains
REVERT: A  125 MET cc_start: 0.8876 (mpp) cc_final: 0.8325 (mpp)
REVERT: A  233 SER cc_start: 0.8957 (m) cc_final: 0.8220 (t)
REVERT: A  279 MET cc_start: 0.6915 (ttp) cc_final: 0.6387 (tmm)
REVERT: A  400 TRP cc_start: 0.8278 (t60) cc_final: 0.7934 (t-100)
REVERT: A  420 MET cc_start: 0.8854 (mmm) cc_final: 0.8510 (tpp)
REVERT: B   61 LYS cc_start: 0.8785 (mttp) cc_final: 0.8516 (mmmt)
REVERT: B  271 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7720 (tp)
REVERT: C  224 ARG cc_start: 0.8920 (tmm-80) cc_final: 0.8589 (tmm-80)
REVERT: D   63 THR cc_start: 0.9398 (m) cc_final: 0.9130 (m)
REVERT: D   88 MET cc_start: 0.8670 (ttp) cc_final: 0.8322 (tmm)
REVERT: D  187 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8935 (pp)
REVERT: D  219 ASP cc_start: 0.9064 (m-30) cc_final: 0.8784 (m-30)
REVERT: E   20 TRP cc_start: 0.8544 (m100) cc_final: 0.8047 (m-10)
REVERT: E   83 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8778 (mt-10)
REVERT: E   88 MET cc_start: 0.8832 (tpp) cc_final: 0.8580 (tpt)
  outliers start: 27
  outliers final: 21
  residues processed: 118
  average time/residue: 0.2029
  time to fit residues: 36.7714
Evaluate side-chains
  116 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 122 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 132 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 119 optimal weight:    0.6980
   chunk 133 optimal weight:    0.7980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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**
** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.061805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.049165 restraints weight = 47387.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.050941 restraints weight = 21746.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.052122 restraints weight = 13311.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11871  Z= 0.131
  Angle     :  0.617  10.630  16116  Z= 0.299
  Chirality :  0.043   0.207   1861
  Planarity :  0.003   0.036   2063
  Dihedral  :  4.679  42.748   1645
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.83 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.23), residues: 1498
  helix:  1.17 (0.21), residues: 669
  sheet: -1.74 (0.39), residues: 188
  loop : -1.65 (0.25), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 
 PHE   0.013   0.001   PHE A 110 
 TYR   0.028   0.002   TYR C  78 
 ARG   0.002   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02851 (  483)
  hydrogen bonds       : angle       3.87440 ( 1359)
  covalent geometry    : bond        0.00299 (11871)
  covalent geometry    : angle       0.61697 (16116)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.596 
Fit side-chains
REVERT: A  125 MET cc_start: 0.8879 (mpp) cc_final: 0.8303 (mpp)
REVERT: A  233 SER cc_start: 0.8871 (m) cc_final: 0.8130 (t)
REVERT: A  400 TRP cc_start: 0.8138 (t60) cc_final: 0.7844 (t-100)
REVERT: A  420 MET cc_start: 0.8829 (mmm) cc_final: 0.8507 (tpp)
REVERT: B   61 LYS cc_start: 0.8806 (mttp) cc_final: 0.8552 (mmmt)
REVERT: B  271 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7763 (tp)
REVERT: C   78 TYR cc_start: 0.8753 (t80) cc_final: 0.8310 (t80)
REVERT: C  224 ARG cc_start: 0.8915 (tmm-80) cc_final: 0.8608 (tmm-80)
REVERT: D   63 THR cc_start: 0.9390 (m) cc_final: 0.9101 (m)
REVERT: D   88 MET cc_start: 0.8561 (ttp) cc_final: 0.8091 (tmm)
REVERT: D  170 GLU cc_start: 0.7019 (pm20) cc_final: 0.6727 (mp0)
REVERT: D  187 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8874 (pp)
REVERT: D  219 ASP cc_start: 0.9072 (m-30) cc_final: 0.8764 (m-30)
REVERT: E   20 TRP cc_start: 0.8517 (m100) cc_final: 0.7982 (m-10)
REVERT: E   83 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8776 (mt-10)
REVERT: E   88 MET cc_start: 0.8781 (tpp) cc_final: 0.8507 (tpt)
REVERT: E  219 ASP cc_start: 0.8506 (m-30) cc_final: 0.7999 (m-30)
REVERT: E  221 TYR cc_start: 0.9151 (t80) cc_final: 0.8789 (t80)
  outliers start: 23
  outliers final: 20
  residues processed: 121
  average time/residue: 0.2911
  time to fit residues: 55.5797
Evaluate side-chains
  116 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  187 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 66 optimal weight:    0.1980
   chunk 22 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 146 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3294 r_free = 0.3294 target = 0.061972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.049575 restraints weight = 46723.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.051304 restraints weight = 21826.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.052482 restraints weight = 13468.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11871  Z= 0.124
  Angle     :  0.621  11.321  16116  Z= 0.301
  Chirality :  0.043   0.182   1861
  Planarity :  0.003   0.036   2063
  Dihedral  :  4.654  42.278   1645
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 21.08 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.23), residues: 1498
  helix:  1.29 (0.22), residues: 667
  sheet: -1.74 (0.38), residues: 195
  loop : -1.63 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 400 
 HIS   0.004   0.001   HIS B 245 
 PHE   0.013   0.001   PHE A 110 
 TYR   0.026   0.001   TYR C  78 
 ARG   0.008   0.000   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02853 (  483)
  hydrogen bonds       : angle       3.84629 ( 1359)
  covalent geometry    : bond        0.00284 (11871)
  covalent geometry    : angle       0.62144 (16116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3677.13 seconds
wall clock time: 66 minutes 34.09 seconds (3994.09 seconds total)