Starting phenix.real_space_refine
on Mon Nov 17 17:32:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e7c_8998/11_2025/6e7c_8998.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e7c_8998/11_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_8998/11_2025/6e7c_8998.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e7c_8998/11_2025/6e7c_8998.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e7c_8998/11_2025/6e7c_8998.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e7c_8998/11_2025/6e7c_8998.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 1.86, per 1000 atoms: 0.27
  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: 0.61
  Conformation dependent library (CDL) restraints added in 363.3 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: 0.25
  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: 1.20

  Time building geometry restraints manager: 0.82 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:             13.340
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.890
  Find NCS groups from input model:        0.040
  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:1.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.320
-------------------------------------------------------------------------------
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= 0.292
  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 : 7.66
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG A  64 
 TYR   0.017   0.002   TYR B  50 
 PHE   0.016   0.002   PHE A 169 
 TRP   0.017   0.003   TRP A 388 
 HIS   0.011   0.002   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 ( 6934)
  covalent geometry    : angle       0.84655 ( 9417)
  hydrogen bonds       : bond        0.30612 (  245)
  hydrogen bonds       : angle      10.15279 (  747)

*********************** 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  : 0.288 
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: 0.6126 (pt)
REVERT: A  188 ILE cc_start: 0.6807 (pp) cc_final: 0.6470 (pt)
REVERT: A  285 GLN cc_start: 0.7785 (pm20) cc_final: 0.6562 (mm110)
REVERT: A  346 TRP cc_start: 0.6759 (p-90) cc_final: 0.5915 (m-10)
REVERT: A  351 PHE cc_start: 0.6785 (m-80) cc_final: 0.6186 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1105
  time to fit residues: 27.4125
Evaluate side-chains
  120 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 292 GLN ** 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 = 0.4160 r_free = 0.4160 target = 0.144197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.123362 restraints weight = 9693.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.127933 restraints weight = 5138.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.131023 restraints weight = 3297.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.133158 restraints weight = 2382.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.134566 restraints weight = 1858.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6934  Z= 0.163
  Angle     :  0.680   7.982   9417  Z= 0.349
  Chirality :  0.047   0.157   1027
  Planarity :  0.005   0.044   1224
  Dihedral  : 12.742 170.795    974
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.26 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.26), residues: 848
  helix: -1.81 (0.23), residues: 367
  sheet: -3.10 (0.42), residues: 123
  loop : -1.72 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 320 
 TYR   0.011   0.002   TYR B 159 
 PHE   0.031   0.002   PHE A 255 
 TRP   0.025   0.003   TRP B 344 
 HIS   0.010   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6934)
  covalent geometry    : angle       0.67997 ( 9417)
  hydrogen bonds       : bond        0.04765 (  245)
  hydrogen bonds       : angle       5.69634 (  747)

*********************** 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
  161 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 MET cc_start: 0.8338 (mmp) cc_final: 0.7906 (mmp)
REVERT: B  200 TYR cc_start: 0.6977 (m-10) cc_final: 0.6636 (m-10)
REVERT: B  247 ASN cc_start: 0.8269 (m-40) cc_final: 0.7731 (m-40)
REVERT: A   90 GLU cc_start: 0.6935 (tt0) cc_final: 0.6534 (tp30)
REVERT: A  188 ILE cc_start: 0.6144 (pp) cc_final: 0.5793 (pt)
REVERT: A  192 HIS cc_start: 0.7791 (t-90) cc_final: 0.7436 (t-170)
REVERT: A  285 GLN cc_start: 0.7668 (pm20) cc_final: 0.6595 (mm110)
REVERT: A  351 PHE cc_start: 0.7306 (m-80) cc_final: 0.6890 (m-80)
REVERT: A  380 ASN cc_start: 0.6600 (t0) cc_final: 0.6268 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 156
  average time/residue: 0.0941
  time to fit residues: 19.2454
Evaluate side-chains
  122 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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   80 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 292 GLN ** 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 = 0.4084 r_free = 0.4084 target = 0.137925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.117932 restraints weight = 9949.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.122318 restraints weight = 5219.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.125318 restraints weight = 3335.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.127324 restraints weight = 2398.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.128779 restraints weight = 1874.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.4027

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= 0.153
  Angle     :  0.658  13.980   9417  Z= 0.328
  Chirality :  0.045   0.147   1027
  Planarity :  0.005   0.042   1224
  Dihedral  : 12.224 173.414    974
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.13 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.27), residues: 848
  helix: -1.29 (0.25), residues: 367
  sheet: -2.58 (0.42), residues: 130
  loop : -1.46 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 320 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.037   0.002   PHE A 255 
 TRP   0.035   0.003   TRP B 344 
 HIS   0.009   0.001   HIS A  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6934)
  covalent geometry    : angle       0.65798 ( 9417)
  hydrogen bonds       : bond        0.03943 (  245)
  hydrogen bonds       : angle       5.04172 (  747)

*********************** 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
  156 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.8245 (m-40) cc_final: 0.7760 (m-40)
REVERT: B  257 MET cc_start: 0.8488 (ptp) cc_final: 0.8265 (ptp)
REVERT: A   75 ILE cc_start: 0.7202 (mp) cc_final: 0.6996 (mt)
REVERT: A  188 ILE cc_start: 0.6437 (pp) cc_final: 0.6139 (pt)
REVERT: A  192 HIS cc_start: 0.7797 (t-90) cc_final: 0.7507 (t-170)
REVERT: A  285 GLN cc_start: 0.7694 (pm20) cc_final: 0.6644 (mm110)
  outliers start: 17
  outliers final: 9
  residues processed: 151
  average time/residue: 0.0879
  time to fit residues: 17.9479
Evaluate side-chains
  128 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  313 VAL
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  328 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 GLN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.138544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.119282 restraints weight = 10036.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.123500 restraints weight = 5262.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.126434 restraints weight = 3376.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.128464 restraints weight = 2426.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.129895 restraints weight = 1884.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.4434

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= 0.136
  Angle     :  0.652  10.615   9417  Z= 0.321
  Chirality :  0.045   0.158   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.806 172.806    974
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.05 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.27), residues: 848
  helix: -0.98 (0.26), residues: 367
  sheet: -2.29 (0.43), residues: 130
  loop : -1.44 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 320 
 TYR   0.012   0.001   TYR B 159 
 PHE   0.023   0.002   PHE A 244 
 TRP   0.032   0.002   TRP B 344 
 HIS   0.007   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6934)
  covalent geometry    : angle       0.65193 ( 9417)
  hydrogen bonds       : bond        0.03534 (  245)
  hydrogen bonds       : angle       4.75028 (  747)

*********************** 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
  154 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 SER cc_start: 0.7029 (m) cc_final: 0.6718 (t)
REVERT: B  247 ASN cc_start: 0.8026 (m-40) cc_final: 0.7356 (m-40)
REVERT: B  257 MET cc_start: 0.8390 (ptp) cc_final: 0.8184 (ptp)
REVERT: B  300 MET cc_start: 0.7912 (mmt) cc_final: 0.7648 (mmt)
REVERT: A  188 ILE cc_start: 0.6397 (pp) cc_final: 0.6126 (pt)
REVERT: A  192 HIS cc_start: 0.7652 (t-90) cc_final: 0.7412 (t-170)
REVERT: A  282 TYR cc_start: 0.7789 (m-80) cc_final: 0.7581 (m-10)
REVERT: A  313 MET cc_start: 0.6919 (mtt) cc_final: 0.6607 (mtt)
REVERT: A  326 LYS cc_start: 0.4474 (mttt) cc_final: 0.4242 (mttp)
REVERT: A  339 ARG cc_start: 0.7158 (mmp-170) cc_final: 0.6878 (mmp80)
REVERT: A  415 GLU cc_start: 0.5875 (pp20) cc_final: 0.5549 (pp20)
  outliers start: 20
  outliers final: 13
  residues processed: 149
  average time/residue: 0.0827
  time to fit residues: 16.8796
Evaluate side-chains
  129 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  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   80 THR
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 75 optimal weight:    0.2980
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
B 105 HIS
B 131 GLN
B 204 ASN
B 226 ASN
B 227 HIS
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 348 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.125829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.105577 restraints weight = 10154.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.109819 restraints weight = 5019.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.112841 restraints weight = 3111.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.114927 restraints weight = 2185.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.116452 restraints weight = 1672.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.4845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6934  Z= 0.164
  Angle     :  0.665   9.451   9417  Z= 0.327
  Chirality :  0.045   0.152   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.626 170.172    974
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.69 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.28), residues: 848
  helix: -0.62 (0.27), residues: 358
  sheet: -1.99 (0.44), residues: 128
  loop : -1.43 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 320 
 TYR   0.016   0.001   TYR B 159 
 PHE   0.017   0.002   PHE B 133 
 TRP   0.031   0.002   TRP B 344 
 HIS   0.008   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6934)
  covalent geometry    : angle       0.66501 ( 9417)
  hydrogen bonds       : bond        0.03553 (  245)
  hydrogen bonds       : angle       4.78222 (  747)

*********************** 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
  147 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 SER cc_start: 0.7031 (m) cc_final: 0.6518 (t)
REVERT: B  328 GLU cc_start: 0.7820 (pt0) cc_final: 0.7606 (mt-10)
REVERT: A   35 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7696 (mm-40)
REVERT: A  188 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6650 (pt)
REVERT: A  192 HIS cc_start: 0.7971 (t-90) cc_final: 0.7723 (t-170)
REVERT: A  339 ARG cc_start: 0.7158 (mmp-170) cc_final: 0.6837 (mmp80)
  outliers start: 24
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0857
  time to fit residues: 16.2751
Evaluate side-chains
  137 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
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  313 VAL
Chi-restraints excluded: chain B residue  363 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   35 GLN
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  188 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 GLN
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.123004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.102590 restraints weight = 10259.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.106791 restraints weight = 5093.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.109802 restraints weight = 3168.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.111797 restraints weight = 2238.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.113233 restraints weight = 1734.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6934  Z= 0.166
  Angle     :  0.678   9.936   9417  Z= 0.331
  Chirality :  0.046   0.190   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.537 167.080    974
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.42 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.28), residues: 848
  helix: -0.51 (0.27), residues: 360
  sheet: -2.08 (0.43), residues: 130
  loop : -1.45 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 214 
 TYR   0.021   0.001   TYR B 159 
 PHE   0.015   0.002   PHE A  67 
 TRP   0.032   0.003   TRP B 344 
 HIS   0.006   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 6934)
  covalent geometry    : angle       0.67812 ( 9417)
  hydrogen bonds       : bond        0.03555 (  245)
  hydrogen bonds       : angle       4.79398 (  747)

*********************** 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
  147 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 SER cc_start: 0.7206 (m) cc_final: 0.6697 (t)
REVERT: B  328 GLU cc_start: 0.7852 (pt0) cc_final: 0.7599 (mt-10)
REVERT: A    5 ILE cc_start: 0.8064 (pp) cc_final: 0.7751 (pt)
REVERT: A   35 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7726 (mm-40)
REVERT: A  182 VAL cc_start: 0.8549 (m) cc_final: 0.8074 (p)
REVERT: A  188 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6775 (pt)
REVERT: A  339 ARG cc_start: 0.7164 (mmp-170) cc_final: 0.6875 (mmp80)
  outliers start: 25
  outliers final: 17
  residues processed: 141
  average time/residue: 0.0813
  time to fit residues: 15.8807
Evaluate side-chains
  134 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  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   35 GLN
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  150 THR
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  328 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  424 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0020
   chunk 82 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    1.2392

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4034 r_free = 0.4034 target = 0.133474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.113865 restraints weight = 10003.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.118035 restraints weight = 5261.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.120873 restraints weight = 3368.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.122875 restraints weight = 2443.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.124183 restraints weight = 1907.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.5355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6934  Z= 0.137
  Angle     :  0.668  10.635   9417  Z= 0.324
  Chirality :  0.044   0.146   1027
  Planarity :  0.004   0.045   1224
  Dihedral  : 11.377 164.647    974
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.78 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.28), residues: 848
  helix: -0.46 (0.27), residues: 364
  sheet: -2.11 (0.43), residues: 128
  loop : -1.48 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 221 
 TYR   0.014   0.001   TYR A 103 
 PHE   0.026   0.002   PHE A 351 
 TRP   0.035   0.003   TRP B 344 
 HIS   0.012   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6934)
  covalent geometry    : angle       0.66756 ( 9417)
  hydrogen bonds       : bond        0.03300 (  245)
  hydrogen bonds       : angle       4.63705 (  747)

*********************** 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
  152 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 VAL cc_start: 0.8369 (m) cc_final: 0.7927 (p)
REVERT: A  188 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6561 (pt)
REVERT: A  352 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7230 (mmtt)
REVERT: A  376 CYS cc_start: 0.7957 (t) cc_final: 0.7753 (t)
  outliers start: 23
  outliers final: 15
  residues processed: 145
  average time/residue: 0.0796
  time to fit residues: 16.0472
Evaluate side-chains
  133 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  180 VAL
Chi-restraints excluded: chain B residue  233 MET
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  188 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.128801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.109316 restraints weight = 10243.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.113216 restraints weight = 5382.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.115988 restraints weight = 3501.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.117937 restraints weight = 2552.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.119153 restraints weight = 2009.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6934  Z= 0.187
  Angle     :  0.721  11.346   9417  Z= 0.348
  Chirality :  0.046   0.145   1027
  Planarity :  0.005   0.044   1224
  Dihedral  : 11.440 162.263    974
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.29 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.28), residues: 848
  helix: -0.54 (0.27), residues: 369
  sheet: -1.95 (0.43), residues: 130
  loop : -1.45 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 214 
 TYR   0.019   0.002   TYR A 103 
 PHE   0.015   0.002   PHE A  67 
 TRP   0.050   0.003   TRP B 344 
 HIS   0.007   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 6934)
  covalent geometry    : angle       0.72102 ( 9417)
  hydrogen bonds       : bond        0.03560 (  245)
  hydrogen bonds       : angle       4.75872 (  747)

*********************** 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
  142 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  191 GLN cc_start: 0.7287 (mp10) cc_final: 0.7043 (mp10)
REVERT: A  182 VAL cc_start: 0.8492 (m) cc_final: 0.8092 (p)
  outliers start: 21
  outliers final: 18
  residues processed: 134
  average time/residue: 0.0789
  time to fit residues: 14.5673
Evaluate side-chains
  132 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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  180 VAL
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  293 MET
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  150 THR
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  378 LEU
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 83 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.114697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.094732 restraints weight = 10549.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.098619 restraints weight = 5310.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.101315 restraints weight = 3346.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.103216 restraints weight = 2408.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.104552 restraints weight = 1884.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.6004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   6934  Z= 0.260
  Angle     :  0.806  12.147   9417  Z= 0.398
  Chirality :  0.049   0.150   1027
  Planarity :  0.005   0.043   1224
  Dihedral  : 11.736 162.720    974
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 18.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.29 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.28), residues: 848
  helix: -0.67 (0.27), residues: 371
  sheet: -2.17 (0.42), residues: 134
  loop : -1.57 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 320 
 TYR   0.019   0.002   TYR A 103 
 PHE   0.035   0.002   PHE A 351 
 TRP   0.036   0.003   TRP B 344 
 HIS   0.005   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 ( 6934)
  covalent geometry    : angle       0.80554 ( 9417)
  hydrogen bonds       : bond        0.04036 (  245)
  hydrogen bonds       : angle       5.04177 (  747)

*********************** 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
  142 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.8280 (pp) cc_final: 0.7981 (pt)
REVERT: A  182 VAL cc_start: 0.8773 (m) cc_final: 0.8355 (p)
REVERT: A  370 LYS cc_start: 0.8833 (tttp) cc_final: 0.8502 (tptt)
REVERT: A  425 MET cc_start: 0.8518 (mmm) cc_final: 0.8311 (tpp)
  outliers start: 23
  outliers final: 19
  residues processed: 135
  average time/residue: 0.0800
  time to fit residues: 14.8674
Evaluate side-chains
  126 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
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  131 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  293 MET
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  150 THR
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  378 LEU
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 20 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0470
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.2084

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 227 HIS
** 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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.119917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.100138 restraints weight = 10311.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.104103 restraints weight = 5155.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.106894 restraints weight = 3231.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.108851 restraints weight = 2308.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.110226 restraints weight = 1792.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.6103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6934  Z= 0.146
  Angle     :  0.744  11.643   9417  Z= 0.360
  Chirality :  0.046   0.176   1027
  Planarity :  0.005   0.044   1224
  Dihedral  : 11.358 163.504    974
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 20.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.28), residues: 848
  helix: -0.61 (0.26), residues: 377
  sheet: -2.06 (0.44), residues: 129
  loop : -1.53 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 221 
 TYR   0.014   0.001   TYR A  24 
 PHE   0.028   0.002   PHE B 133 
 TRP   0.043   0.003   TRP B 344 
 HIS   0.009   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6934)
  covalent geometry    : angle       0.74351 ( 9417)
  hydrogen bonds       : bond        0.03366 (  245)
  hydrogen bonds       : angle       4.82908 (  747)

********************** 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
  134 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 MET cc_start: 0.7780 (mmm) cc_final: 0.7536 (mmp)
REVERT: B  312 THR cc_start: 0.8761 (m) cc_final: 0.8519 (p)
REVERT: A  182 VAL cc_start: 0.8691 (m) cc_final: 0.8288 (p)
REVERT: A  413 MET cc_start: 0.7762 (pmm) cc_final: 0.7317 (pmm)
REVERT: A  424 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8536 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0809
  time to fit residues: 14.2607
Evaluate side-chains
  126 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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  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  150 THR
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  378 LEU
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 18 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0070
   chunk 65 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.8004

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** 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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.132808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.113194 restraints weight = 10099.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.117318 restraints weight = 5307.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.120090 restraints weight = 3423.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.122100 restraints weight = 2499.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.123482 restraints weight = 1954.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.6141

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= 0.131
  Angle     :  0.724  11.299   9417  Z= 0.349
  Chirality :  0.045   0.148   1027
  Planarity :  0.005   0.043   1224
  Dihedral  : 11.124 162.563    974
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.93 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.28), residues: 848
  helix: -0.46 (0.27), residues: 377
  sheet: -1.87 (0.44), residues: 129
  loop : -1.52 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 221 
 TYR   0.013   0.001   TYR A 357 
 PHE   0.022   0.002   PHE B 133 
 TRP   0.040   0.003   TRP B 344 
 HIS   0.009   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6934)
  covalent geometry    : angle       0.72391 ( 9417)
  hydrogen bonds       : bond        0.03371 (  245)
  hydrogen bonds       : angle       4.75734 (  747)

===============================================================================
Job complete
usr+sys time: 1478.12 seconds
wall clock time: 26 minutes 23.80 seconds (1583.80 seconds total)