Starting phenix.real_space_refine
on Wed Feb 12 02:05:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e7c_8998/02_2025/6e7c_8998.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e7c_8998/02_2025/6e7c_8998.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e7c_8998/02_2025/6e7c_8998.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e7c_8998/02_2025/6e7c_8998.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e7c_8998/02_2025/6e7c_8998.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e7c_8998/02_2025/6e7c_8998.cif"
  }
  resolution = 3.65
  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
-------------------------------------------------------------------------------
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=   0.228 sd=   1.115
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    4259      2.51       5
     N    1156      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6780
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3356
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3358
          Classifications: {'peptide': 428}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.02, per 1000 atoms: 1.04
  Number of scatterers: 6780
  At special positions: 0
  Unit cell: (74, 73, 107, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      49     16.00
     P       6     15.00
     Mg      2     11.99
     O    1308      8.00
     N    1156      7.00
     C    4259      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: 1.89
  Conformation dependent library (CDL) restraints added in 959.5 milliseconds
  

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1582

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      49.9% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 28
      removed outlier: 3.644A  pdb=" N   GLN B  15 " --> pdb=" O   GLN B  11 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP B  26 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 49
      removed outlier: 3.694A  pdb=" N   VAL B  49 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 46 through 49'
    Processing helix  chain 'B' and resid 69 through 79
      removed outlier: 3.967A  pdb=" N   MET B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   SER B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 100
      removed outlier: 4.157A  pdb=" N   ASN B  99 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 3.832A  pdb=" N   ASP B 118 " --> pdb=" O   ASP B 114 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   VAL B 119 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B 120 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
      removed outlier: 3.588A  pdb=" N   GLY B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 159
      removed outlier: 3.555A  pdb=" N   LEU B 151 " --> pdb=" O   MET B 147 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG B 156 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLU B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.556A  pdb=" N   LEU B 187 " --> pdb=" O   TYR B 183 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   HIS B 190 " --> pdb=" O   THR B 186 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 213
      removed outlier: 3.665A  pdb=" N   ASP B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 226
    Processing helix  chain 'B' and resid 226 through 242
      removed outlier: 3.548A  pdb=" N   ALA B 231 " --> pdb=" O   HIS B 227 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   MET B 233 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL B 236 " --> pdb=" O   THR B 232 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 256
    Processing helix  chain 'B' and resid 276 through 280
      removed outlier: 3.575A  pdb=" N   GLN B 279 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLN B 280 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 276 through 280'
    Processing helix  chain 'B' and resid 285 through 295
      removed outlier: 3.618A  pdb=" N   GLN B 292 " --> pdb=" O   GLU B 288 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   MET B 293 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.544A  pdb=" N   GLN B 329 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   MET B 330 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 390
      removed outlier: 4.146A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLN B 384 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ALA B 387 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 400
      removed outlier: 3.778A  pdb=" N   TYR B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 424
      removed outlier: 4.128A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLU B 421 " --> pdb=" O   ASP B 417 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 28
      removed outlier: 3.509A  pdb=" N   VAL A  14 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA A  19 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU A  22 " --> pdb=" O   ASN A  18 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR A  24 " --> pdb=" O   CYS A  20 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU A  26 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
      removed outlier: 3.663A  pdb=" N   THR A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
    Processing helix  chain 'A' and resid 102 through 108
      removed outlier: 3.822A  pdb=" N   TYR A 108 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 129
      removed outlier: 4.222A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ASP A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 3.572A  pdb=" N   PHE A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLU A 155 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 198
      removed outlier: 3.520A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ILE A 188 " --> pdb=" O   PRO A 184 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   GLU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 216
      removed outlier: 3.747A  pdb=" N   TYR A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG A 215 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.682A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLN A 233 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 3.790A  pdb=" N   PHE A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   THR A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 260 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.763A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 294
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 4.217A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LYS A 336 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.860A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ARG A 390 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   HIS A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   MET A 398 " --> pdb=" O   LYS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 412
      removed outlier: 4.468A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 437
      removed outlier: 3.719A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   TYR A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 66
      removed outlier: 8.986A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   PHE B 133 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   LEU B 135 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 5.684A  pdb=" N   HIS B 137 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54
      removed outlier: 3.501A  pdb=" N   VAL B  60 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS B  58 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 170
    Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 200
      removed outlier: 6.771A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93
      removed outlier: 8.381A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   GLU A   3 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   GLY A 134 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ILE A   5 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 167 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS A 139 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93
      removed outlier: 8.381A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   GLU A   3 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   GLY A 134 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ILE A   5 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 167 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS A 139 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 55 through 56
    Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 273
      removed outlier: 3.608A  pdb=" N   ALA A 374 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 316 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   CYS A 316 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    747 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 2.03 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: 2228
        1.34 -     1.46: 1131
        1.46 -     1.57: 3485
        1.57 -     1.69: 10
        1.69 -     1.81: 80
  Bond restraints: 6934
  Sorted by residual:
  bond pdb=" O3B G2P B 502 "
       pdb=" PG  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.716  1.603  0.113 2.00e-02 2.50e+03 3.22e+01
  bond pdb=" O1A G2P B 502 "
       pdb=" PA  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.507  1.608 -0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" O1B G2P B 502 "
       pdb=" PB  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.510  1.608 -0.098 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" C5  GTP A 502 "
       pdb=" C6  GTP A 502 "
    ideal  model  delta    sigma   weight residual
    1.390  1.479 -0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" C4  G2P B 502 "
       pdb=" C5  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.384  1.463 -0.079 2.00e-02 2.50e+03 1.56e+01
  ... (remaining 6929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 9235
        2.48 -     4.96: 152
        4.96 -     7.44: 18
        7.44 -     9.92: 8
        9.92 -    12.40: 4
  Bond angle restraints: 9417
  Sorted by residual:
  angle pdb=" C3A G2P B 502 "
        pdb=" PA  G2P B 502 "
        pdb=" O5' G2P B 502 "
      ideal   model   delta    sigma   weight residual
      99.14  111.54  -12.40 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" PA  G2P B 502 "
        pdb=" C3A G2P B 502 "
        pdb=" PB  G2P B 502 "
      ideal   model   delta    sigma   weight residual
     120.83  108.52   12.31 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" O1B GTP A 502 "
        pdb=" PB  GTP A 502 "
        pdb=" O2B GTP A 502 "
      ideal   model   delta    sigma   weight residual
     109.50  120.92  -11.42 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" O1A GTP A 502 "
        pdb=" PA  GTP A 502 "
        pdb=" O2A GTP A 502 "
      ideal   model   delta    sigma   weight residual
     109.50  120.33  -10.83 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" C   LEU A 217 "
        pdb=" N   ASP A 218 "
        pdb=" CA  ASP A 218 "
      ideal   model   delta    sigma   weight residual
     122.82  127.24   -4.42 1.42e+00 4.96e-01 9.68e+00
  ... (remaining 9412 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.38: 4092
       33.38 -    66.77: 41
       66.77 -   100.15: 8
      100.15 -   133.54: 1
      133.54 -   166.92: 3
  Dihedral angle restraints: 4145
    sinusoidal: 1678
      harmonic: 2467
  Sorted by residual:
  dihedral pdb=" C4' GTP A 502 "
           pdb=" C5' GTP A 502 "
           pdb=" O5' GTP A 502 "
           pdb=" PA  GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87   93.95  166.92     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" C8  GTP A 502 "
           pdb=" C1' GTP A 502 "
           pdb=" N9  GTP A 502 "
           pdb=" O4' GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -62.13  166.73     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" O2G GTP A 502 "
           pdb=" O3B GTP A 502 "
           pdb=" PG  GTP A 502 "
           pdb=" PB  GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -35.43 -147.27     1      2.00e+01 2.50e-03 4.42e+01
  ... (remaining 4142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 600
       0.032 -    0.064: 284
       0.064 -    0.096: 82
       0.096 -    0.128: 53
       0.128 -    0.160: 8
  Chirality restraints: 1027
  Sorted by residual:
  chirality pdb=" CA  ILE B 368 "
            pdb=" N   ILE B 368 "
            pdb=" C   ILE B 368 "
            pdb=" CB  ILE B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  VAL A 324 "
            pdb=" N   VAL A 324 "
            pdb=" C   VAL A 324 "
            pdb=" CB  VAL A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  ASP A 218 "
            pdb=" N   ASP A 218 "
            pdb=" C   ASP A 218 "
            pdb=" CB  ASP A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.34e-01
  ... (remaining 1024 not shown)

  Planarity restraints: 1224
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  69 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO B  70 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B  70 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  70 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 221 "    0.029 5.00e-02 4.00e+02   4.33e-02 3.00e+00
        pdb=" N   PRO A 222 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 222 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 222 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 391 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   ARG B 391 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ARG B 391 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS B 392 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1221 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 56
        2.50 -     3.10: 5419
        3.10 -     3.70: 10570
        3.70 -     4.30: 15925
        4.30 -     4.90: 25485
  Nonbonded interactions: 57455
  Sorted by model distance:
  nonbonded pdb="MG    MG B 501 "
            pdb=" O2B G2P B 502 "
     model   vdw
     1.901 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O2G GTP A 502 "
     model   vdw
     1.946 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O1B GTP A 502 "
     model   vdw
     2.028 2.170
  nonbonded pdb=" O1A G2P B 502 "
            pdb=" O1B G2P B 502 "
     model   vdw
     2.078 3.040
  nonbonded pdb="MG    MG B 501 "
            pdb=" O1G G2P B 502 "
     model   vdw
     2.127 2.170
  ... (remaining 57450 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             7.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     22.080
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
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      :  0.007   0.113   6934  Z= 0.423
  Angle     :  0.847  12.404   9417  Z= 0.408
  Chirality :  0.045   0.160   1027
  Planarity :  0.005   0.045   1224
  Dihedral  : 12.698 166.923   2563
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -4.32 (0.25), residues: 848
  helix: -3.40 (0.17), residues: 343
  sheet: -3.87 (0.36), residues: 130
  loop : -1.67 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP A 388 
 HIS   0.011   0.002   HIS B   6 
 PHE   0.016   0.002   PHE A 169 
 TYR   0.017   0.002   TYR B  50 
 ARG   0.008   0.001   ARG A  64 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 ILE cc_start: 0.6379 (pt) cc_final: 0.6129 (pt)
REVERT: A  188 ILE cc_start: 0.6807 (pp) cc_final: 0.6453 (pt)
REVERT: A  285 GLN cc_start: 0.7785 (pm20) cc_final: 0.6558 (mm110)
REVERT: A  346 TRP cc_start: 0.6759 (p-90) cc_final: 0.5916 (m-10)
REVERT: A  351 PHE cc_start: 0.6785 (m-80) cc_final: 0.6180 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2260
  time to fit residues: 55.7088
Evaluate side-chains
  121 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 396 HIS
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 ASN
A 356 ASN
A 358 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.148240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.127463 restraints weight = 9571.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.132027 restraints weight = 5089.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.135189 restraints weight = 3272.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6934  Z= 0.219
  Angle     :  0.679   8.056   9417  Z= 0.348
  Chirality :  0.046   0.156   1027
  Planarity :  0.005   0.045   1224
  Dihedral  : 12.543 169.429    974
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.26 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -3.19 (0.26), residues: 848
  helix: -1.86 (0.23), residues: 376
  sheet: -3.04 (0.42), residues: 123
  loop : -1.81 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP B 344 
 HIS   0.010   0.001   HIS B   6 
 PHE   0.031   0.002   PHE A 255 
 TYR   0.016   0.002   TYR B 159 
 ARG   0.005   0.001   ARG B 320 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.8063 (m-40) cc_final: 0.7477 (m-40)
REVERT: A   35 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7759 (mm110)
REVERT: A   90 GLU cc_start: 0.6868 (tt0) cc_final: 0.6502 (tp30)
REVERT: A  192 HIS cc_start: 0.7810 (t-90) cc_final: 0.7480 (t-170)
REVERT: A  285 GLN cc_start: 0.7669 (pm20) cc_final: 0.6604 (mm110)
REVERT: A  351 PHE cc_start: 0.7206 (m-80) cc_final: 0.6838 (m-80)
REVERT: A  380 ASN cc_start: 0.6486 (t0) cc_final: 0.6248 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 156
  average time/residue: 0.2007
  time to fit residues: 41.2446
Evaluate side-chains
  120 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 GLU
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   80 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 75 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
B 100 ASN
B 131 GLN
B 195 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 GLN
A 358 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.136414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.116397 restraints weight = 9979.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.120763 restraints weight = 5236.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.123727 restraints weight = 3344.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6934  Z= 0.253
  Angle     :  0.667  12.822   9417  Z= 0.335
  Chirality :  0.046   0.150   1027
  Planarity :  0.005   0.044   1224
  Dihedral  : 12.087 172.398    974
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.72 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.57 (0.27), residues: 848
  helix: -1.33 (0.25), residues: 368
  sheet: -2.77 (0.42), residues: 127
  loop : -1.47 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B 344 
 HIS   0.007   0.001   HIS B 396 
 PHE   0.018   0.002   PHE B 167 
 TYR   0.010   0.001   TYR B 398 
 ARG   0.006   0.001   ARG B 320 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ILE cc_start: 0.6521 (pp) cc_final: 0.6157 (pt)
REVERT: A  192 HIS cc_start: 0.7914 (t-90) cc_final: 0.7627 (t-170)
  outliers start: 16
  outliers final: 8
  residues processed: 146
  average time/residue: 0.1830
  time to fit residues: 35.7496
Evaluate side-chains
  117 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 49 optimal weight:    0.3980
   chunk 27 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
B 131 GLN
B 190 HIS
B 227 HIS
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 423 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.139903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.120061 restraints weight = 10055.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.124459 restraints weight = 5202.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.127466 restraints weight = 3302.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.4484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6934  Z= 0.182
  Angle     :  0.645  10.312   9417  Z= 0.317
  Chirality :  0.045   0.161   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.719 171.660    974
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.73 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -2.09 (0.27), residues: 848
  helix: -0.85 (0.26), residues: 361
  sheet: -2.26 (0.43), residues: 129
  loop : -1.43 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 344 
 HIS   0.010   0.001   HIS B 190 
 PHE   0.022   0.002   PHE A 244 
 TYR   0.013   0.001   TYR A  24 
 ARG   0.006   0.000   ARG B 320 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  158 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7036 (tt0)
REVERT: B  159 TYR cc_start: 0.7669 (m-80) cc_final: 0.6697 (m-80)
REVERT: B  247 ASN cc_start: 0.7869 (m-40) cc_final: 0.7065 (m-40)
REVERT: B  300 MET cc_start: 0.7861 (mmt) cc_final: 0.7635 (mmt)
REVERT: A  188 ILE cc_start: 0.6132 (pp) cc_final: 0.5839 (pt)
REVERT: A  192 HIS cc_start: 0.7737 (t-90) cc_final: 0.7483 (t-170)
REVERT: A  313 MET cc_start: 0.6906 (mtt) cc_final: 0.6460 (mtt)
REVERT: A  339 ARG cc_start: 0.7313 (mmp-170) cc_final: 0.7001 (mmp80)
REVERT: A  415 GLU cc_start: 0.5982 (pp20) cc_final: 0.5659 (pp20)
  outliers start: 19
  outliers final: 13
  residues processed: 152
  average time/residue: 0.1826
  time to fit residues: 37.4237
Evaluate side-chains
  128 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   chunk 77 optimal weight:    0.0060
   chunk 11 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
B 105 HIS
B 131 GLN
B 226 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 HIS
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 348 ASN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.139840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.120456 restraints weight = 9849.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.124683 restraints weight = 5217.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.127532 restraints weight = 3354.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.4780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6934  Z= 0.169
  Angle     :  0.607   9.264   9417  Z= 0.301
  Chirality :  0.044   0.152   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.480 170.733    974
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.28 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.83 (0.28), residues: 848
  helix: -0.55 (0.27), residues: 358
  sheet: -2.10 (0.43), residues: 132
  loop : -1.40 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 344 
 HIS   0.008   0.001   HIS B   6 
 PHE   0.016   0.002   PHE A 244 
 TYR   0.012   0.001   TYR A 103 
 ARG   0.005   0.001   ARG B 156 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.7808 (m-40) cc_final: 0.6970 (m-40)
REVERT: B  257 MET cc_start: 0.7913 (ptp) cc_final: 0.7625 (ptp)
REVERT: B  300 MET cc_start: 0.7816 (mmt) cc_final: 0.7525 (mmt)
REVERT: A  188 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5818 (pt)
REVERT: A  192 HIS cc_start: 0.7700 (t-90) cc_final: 0.7440 (t-170)
REVERT: A  313 MET cc_start: 0.6946 (mtt) cc_final: 0.6433 (mtt)
REVERT: A  339 ARG cc_start: 0.7118 (mmp-170) cc_final: 0.6857 (mmp80)
REVERT: A  352 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7041 (mmpt)
REVERT: A  380 ASN cc_start: 0.6822 (t0) cc_final: 0.6474 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1797
  time to fit residues: 36.1303
Evaluate side-chains
  136 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  376 CYS
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
B 204 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.138893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.119266 restraints weight = 9979.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.123512 restraints weight = 5238.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.126388 restraints weight = 3359.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6934  Z= 0.175
  Angle     :  0.627  12.624   9417  Z= 0.305
  Chirality :  0.044   0.195   1027
  Planarity :  0.004   0.041   1224
  Dihedral  : 11.287 168.778    974
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.69 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.58 (0.28), residues: 848
  helix: -0.23 (0.28), residues: 353
  sheet: -1.97 (0.43), residues: 135
  loop : -1.38 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP B 344 
 HIS   0.006   0.001   HIS B   6 
 PHE   0.014   0.002   PHE A 244 
 TYR   0.013   0.001   TYR B 159 
 ARG   0.004   0.001   ARG B  77 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5973 (pt)
REVERT: A  192 HIS cc_start: 0.7720 (t-90) cc_final: 0.7489 (t-170)
REVERT: A  305 CYS cc_start: 0.7338 (p) cc_final: 0.6983 (p)
REVERT: A  313 MET cc_start: 0.7014 (mtt) cc_final: 0.6616 (mtt)
REVERT: A  339 ARG cc_start: 0.7141 (mmp-170) cc_final: 0.6890 (mmp80)
REVERT: A  352 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7085 (mmpt)
  outliers start: 21
  outliers final: 13
  residues processed: 141
  average time/residue: 0.1725
  time to fit residues: 33.2194
Evaluate side-chains
  127 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  376 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.138763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.119534 restraints weight = 9809.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.123751 restraints weight = 5145.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.126681 restraints weight = 3294.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.5245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6934  Z= 0.177
  Angle     :  0.626  10.972   9417  Z= 0.306
  Chirality :  0.044   0.148   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.207 166.874    974
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.37 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 (0.28), residues: 848
  helix: -0.16 (0.28), residues: 358
  sheet: -1.80 (0.43), residues: 130
  loop : -1.47 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 344 
 HIS   0.006   0.001   HIS B   6 
 PHE   0.015   0.001   PHE B 408 
 TYR   0.017   0.001   TYR B 159 
 ARG   0.008   0.001   ARG A 214 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ILE cc_start: 0.6296 (OUTLIER) cc_final: 0.6039 (pt)
REVERT: A  192 HIS cc_start: 0.7699 (t-90) cc_final: 0.7455 (t-170)
REVERT: A  313 MET cc_start: 0.7117 (mtt) cc_final: 0.6735 (mtt)
REVERT: A  339 ARG cc_start: 0.7087 (mmp-170) cc_final: 0.6871 (mmp80)
REVERT: A  352 LYS cc_start: 0.7781 (mmmt) cc_final: 0.7079 (mmpt)
  outliers start: 21
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1798
  time to fit residues: 35.5125
Evaluate side-chains
  129 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  378 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0980
   chunk 49 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.140747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.120570 restraints weight = 9794.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.124973 restraints weight = 5131.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.128030 restraints weight = 3293.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.5413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6934  Z= 0.171
  Angle     :  0.632  11.074   9417  Z= 0.309
  Chirality :  0.044   0.149   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.019 163.478    974
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.37 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.48 (0.28), residues: 848
  helix: -0.10 (0.28), residues: 357
  sheet: -1.71 (0.44), residues: 130
  loop : -1.50 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP B 344 
 HIS   0.006   0.001   HIS B   6 
 PHE   0.020   0.001   PHE A 169 
 TYR   0.011   0.001   TYR A 357 
 ARG   0.010   0.001   ARG A 221 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.7598 (m-40) cc_final: 0.6791 (m-40)
REVERT: B  330 MET cc_start: 0.7819 (mtp) cc_final: 0.7573 (mmm)
REVERT: A   50 ASN cc_start: 0.7714 (t0) cc_final: 0.7335 (t0)
REVERT: A  182 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7554 (p)
REVERT: A  188 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6126 (pt)
REVERT: A  192 HIS cc_start: 0.7698 (t-90) cc_final: 0.7483 (t-170)
REVERT: A  313 MET cc_start: 0.7134 (mtt) cc_final: 0.6801 (mtt)
REVERT: A  339 ARG cc_start: 0.7106 (mmp-170) cc_final: 0.6895 (mmp80)
REVERT: A  352 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7158 (mmtt)
REVERT: A  376 CYS cc_start: 0.8020 (t) cc_final: 0.7684 (t)
REVERT: A  377 MET cc_start: 0.8449 (tmm) cc_final: 0.7709 (tmm)
  outliers start: 24
  outliers final: 17
  residues processed: 141
  average time/residue: 0.1778
  time to fit residues: 34.1777
Evaluate side-chains
  135 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0670
   chunk 23 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
B 134 GLN
** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  61 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.131162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.110009 restraints weight = 9899.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114284 restraints weight = 4947.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.117357 restraints weight = 3107.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.5541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6934  Z= 0.192
  Angle     :  0.657  11.684   9417  Z= 0.322
  Chirality :  0.044   0.148   1027
  Planarity :  0.004   0.044   1224
  Dihedral  : 10.867 155.177    974
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.60 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.46 (0.28), residues: 848
  helix: -0.05 (0.28), residues: 358
  sheet: -1.65 (0.44), residues: 131
  loop : -1.55 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 344 
 HIS   0.005   0.001   HIS B   6 
 PHE   0.018   0.001   PHE A 169 
 TYR   0.010   0.001   TYR A 103 
 ARG   0.010   0.001   ARG A 221 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.7801 (m-40) cc_final: 0.6970 (m-40)
REVERT: B  330 MET cc_start: 0.8149 (mtp) cc_final: 0.7766 (mtp)
REVERT: A   50 ASN cc_start: 0.7692 (t0) cc_final: 0.7270 (t0)
REVERT: A  182 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7759 (p)
REVERT: A  313 MET cc_start: 0.7149 (mtt) cc_final: 0.6653 (mtt)
REVERT: A  339 ARG cc_start: 0.7209 (mmp-170) cc_final: 0.6940 (mmp80)
REVERT: A  352 LYS cc_start: 0.7703 (mmmt) cc_final: 0.6873 (mmtt)
REVERT: A  370 LYS cc_start: 0.8388 (tptt) cc_final: 0.7857 (tttp)
REVERT: A  376 CYS cc_start: 0.8131 (t) cc_final: 0.7854 (t)
REVERT: A  377 MET cc_start: 0.8320 (tmm) cc_final: 0.7549 (tmm)
REVERT: A  414 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4471 (pt0)
  outliers start: 19
  outliers final: 15
  residues processed: 134
  average time/residue: 0.1920
  time to fit residues: 34.6311
Evaluate side-chains
  130 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0870
   chunk 42 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0070
   chunk 12 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
B 165 ASN
B 334 GLN
A 192 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.134615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.113026 restraints weight = 10024.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.117520 restraints weight = 5022.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.120708 restraints weight = 3136.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.5724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6934  Z= 0.166
  Angle     :  0.664  11.783   9417  Z= 0.324
  Chirality :  0.044   0.191   1027
  Planarity :  0.004   0.041   1224
  Dihedral  : 10.729 157.059    974
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.02 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.38 (0.28), residues: 848
  helix:  0.00 (0.28), residues: 357
  sheet: -1.67 (0.43), residues: 136
  loop : -1.46 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 344 
 HIS   0.010   0.001   HIS A 192 
 PHE   0.045   0.002   PHE A 169 
 TYR   0.011   0.001   TYR A  24 
 ARG   0.009   0.001   ARG A 214 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.7528 (m-40) cc_final: 0.6659 (m-40)
REVERT: B  330 MET cc_start: 0.8115 (mtp) cc_final: 0.7802 (mtp)
REVERT: A   50 ASN cc_start: 0.7672 (t0) cc_final: 0.7261 (t0)
REVERT: A  182 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.7939 (p)
REVERT: A  313 MET cc_start: 0.7135 (mtt) cc_final: 0.6785 (mtt)
REVERT: A  339 ARG cc_start: 0.7144 (mmp-170) cc_final: 0.6827 (mmp80)
REVERT: A  352 LYS cc_start: 0.7578 (mmmt) cc_final: 0.6819 (mmtt)
REVERT: A  370 LYS cc_start: 0.8353 (tptt) cc_final: 0.7864 (tttp)
REVERT: A  376 CYS cc_start: 0.8139 (t) cc_final: 0.7731 (t)
REVERT: A  377 MET cc_start: 0.8240 (tmm) cc_final: 0.7518 (tmm)
REVERT: A  414 GLU cc_start: 0.4853 (OUTLIER) cc_final: 0.4158 (pt0)
  outliers start: 21
  outliers final: 15
  residues processed: 139
  average time/residue: 0.1751
  time to fit residues: 33.8714
Evaluate side-chains
  131 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  192 HIS
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 60 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    2.4984

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 GLN
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.123040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.102708 restraints weight = 10183.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.106763 restraints weight = 5146.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.109611 restraints weight = 3256.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6934  Z= 0.299
  Angle     :  0.727  11.351   9417  Z= 0.366
  Chirality :  0.048   0.252   1027
  Planarity :  0.005   0.041   1224
  Dihedral  : 11.046 159.798    974
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.97 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 (0.28), residues: 848
  helix: -0.31 (0.28), residues: 365
  sheet: -1.57 (0.44), residues: 131
  loop : -1.42 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.003   TRP B 344 
 HIS   0.020   0.002   HIS A 192 
 PHE   0.047   0.002   PHE A 169 
 TYR   0.016   0.002   TYR B 159 
 ARG   0.010   0.001   ARG A 214 

===============================================================================
Job complete
usr+sys time: 2716.45 seconds
wall clock time: 49 minutes 29.63 seconds (2969.63 seconds total)