Starting phenix.real_space_refine
on Mon Apr 28 05:25:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e7c_8998/04_2025/6e7c_8998.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e7c_8998/04_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_8998/04_2025/6e7c_8998.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e7c_8998/04_2025/6e7c_8998.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e7c_8998/04_2025/6e7c_8998.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e7c_8998/04_2025/6e7c_8998.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.228 sd=   1.115
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    4259      2.51       5
     N    1156      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6780
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3356
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3358
          Classifications: {'peptide': 428}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.60, per 1000 atoms: 0.97
  Number of scatterers: 6780
  At special positions: 0
  Unit cell: (74, 73, 107, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      49     16.00
     P       6     15.00
     Mg      2     11.99
     O    1308      8.00
     N    1156      7.00
     C    4259      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.80
  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: 1.91

  Time building geometry restraints manager: 2.10 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:             11.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.640
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.630
-------------------------------------------------------------------------------
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 : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.32 (0.25), residues: 848
  helix: -3.40 (0.17), residues: 343
  sheet: -3.87 (0.36), residues: 130
  loop : -1.67 (0.33), residues: 375

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

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

*********************** 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  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 ILE cc_start: 0.6379 (pt) cc_final: 0.6129 (pt)
REVERT: A  188 ILE cc_start: 0.6807 (pp) cc_final: 0.6453 (pt)
REVERT: A  285 GLN cc_start: 0.7785 (pm20) cc_final: 0.6558 (mm110)
REVERT: A  346 TRP cc_start: 0.6759 (p-90) cc_final: 0.5916 (m-10)
REVERT: A  351 PHE cc_start: 0.6785 (m-80) cc_final: 0.6180 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2278
  time to fit residues: 56.3301
Evaluate side-chains
  121 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0980
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.148240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.127463 restraints weight = 9571.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.132028 restraints weight = 5089.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.135190 restraints weight = 3272.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6934  Z= 0.149
  Angle     :  0.679   8.056   9417  Z= 0.348
  Chirality :  0.046   0.156   1027
  Planarity :  0.005   0.045   1224
  Dihedral  : 12.543 169.429    974
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.26 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.26), residues: 848
  helix: -1.86 (0.23), residues: 376
  sheet: -3.04 (0.42), residues: 123
  loop : -1.81 (0.31), residues: 349

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04609 (  245)
  hydrogen bonds       : angle       5.66887 (  747)
  covalent geometry    : bond        0.00336 ( 6934)
  covalent geometry    : angle       0.67921 ( 9417)

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

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 ASN cc_start: 0.8063 (m-40) cc_final: 0.7478 (m-40)
REVERT: A   35 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7760 (mm110)
REVERT: A   90 GLU cc_start: 0.6867 (tt0) cc_final: 0.6502 (tp30)
REVERT: A  192 HIS cc_start: 0.7810 (t-90) cc_final: 0.7480 (t-170)
REVERT: A  285 GLN cc_start: 0.7668 (pm20) cc_final: 0.6603 (mm110)
REVERT: A  351 PHE cc_start: 0.7206 (m-80) cc_final: 0.6839 (m-80)
REVERT: A  380 ASN cc_start: 0.6486 (t0) cc_final: 0.6248 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 156
  average time/residue: 0.2007
  time to fit residues: 41.3217
Evaluate side-chains
  120 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 GLU
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   80 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 75 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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  11 GLN
B 100 ASN
B 131 GLN
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 ASN
** 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**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.129757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.110137 restraints weight = 10030.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.114129 restraints weight = 5407.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.116824 restraints weight = 3536.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.4296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   6934  Z= 0.238
  Angle     :  0.741  12.762   9417  Z= 0.374
  Chirality :  0.048   0.154   1027
  Planarity :  0.006   0.054   1224
  Dihedral  : 12.120 172.103    974
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 12.59 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.27), residues: 848
  helix: -1.46 (0.25), residues: 367
  sheet: -2.85 (0.42), residues: 127
  loop : -1.49 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B 344 
 HIS   0.007   0.001   HIS B 396 
 PHE   0.021   0.002   PHE A  67 
 TYR   0.013   0.002   TYR B 398 
 ARG   0.006   0.001   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04491 (  245)
  hydrogen bonds       : angle       5.30713 (  747)
  covalent geometry    : bond        0.00553 ( 6934)
  covalent geometry    : angle       0.74071 ( 9417)

*********************** 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
  161 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  183 TYR cc_start: 0.6956 (m-80) cc_final: 0.6670 (m-80)
REVERT: A   75 ILE cc_start: 0.7701 (mp) cc_final: 0.7487 (mt)
REVERT: A  176 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7876 (mm-40)
REVERT: A  188 ILE cc_start: 0.6894 (pp) cc_final: 0.6554 (pt)
REVERT: A  192 HIS cc_start: 0.7912 (t-90) cc_final: 0.7676 (t-170)
  outliers start: 24
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1826
  time to fit residues: 37.8159
Evaluate side-chains
  119 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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  189 VAL
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  322 SER
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   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0570
   chunk 27 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0770
   chunk 51 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
B 131 GLN
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN
B 227 HIS
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 423 GLN
A  61 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.135088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.115869 restraints weight = 10056.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.119981 restraints weight = 5260.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.122780 restraints weight = 3360.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6934  Z= 0.121
  Angle     :  0.659  10.727   9417  Z= 0.323
  Chirality :  0.045   0.160   1027
  Planarity :  0.004   0.041   1224
  Dihedral  : 11.593 169.703    974
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.14 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.27), residues: 848
  helix: -0.90 (0.26), residues: 363
  sheet: -2.53 (0.43), residues: 128
  loop : -1.47 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 344 
 HIS   0.008   0.001   HIS B 190 
 PHE   0.025   0.002   PHE A 351 
 TYR   0.016   0.001   TYR A  24 
 ARG   0.007   0.001   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  245)
  hydrogen bonds       : angle       4.76828 (  747)
  covalent geometry    : bond        0.00269 ( 6934)
  covalent geometry    : angle       0.65870 ( 9417)

*********************** 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
  152 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 SER cc_start: 0.7083 (m) cc_final: 0.6851 (t)
REVERT: B  257 MET cc_start: 0.8142 (ptp) cc_final: 0.7863 (ptp)
REVERT: B  300 MET cc_start: 0.7869 (mmt) cc_final: 0.7642 (mmt)
REVERT: A  188 ILE cc_start: 0.6430 (pp) cc_final: 0.6122 (pt)
REVERT: A  313 MET cc_start: 0.7013 (mtt) cc_final: 0.6300 (mtt)
REVERT: A  339 ARG cc_start: 0.7101 (mmp-170) cc_final: 0.6787 (mmp80)
  outliers start: 18
  outliers final: 10
  residues processed: 147
  average time/residue: 0.1821
  time to fit residues: 36.1555
Evaluate side-chains
  127 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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  233 MET
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0570
   chunk 7 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 77 optimal weight:    0.3980
   chunk 11 optimal weight:    0.3980
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.3702

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
B 204 ASN
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 348 ASN
A  88 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.132000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.112820 restraints weight = 10012.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.116809 restraints weight = 5298.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.119486 restraints weight = 3419.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.5007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6934  Z= 0.138
  Angle     :  0.638   9.466   9417  Z= 0.313
  Chirality :  0.044   0.145   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.426 168.759    974
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.83 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.27), residues: 848
  helix: -0.60 (0.27), residues: 360
  sheet: -2.40 (0.43), residues: 130
  loop : -1.41 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 344 
 HIS   0.007   0.001   HIS B   6 
 PHE   0.036   0.002   PHE A 255 
 TYR   0.014   0.001   TYR B 159 
 ARG   0.006   0.001   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03320 (  245)
  hydrogen bonds       : angle       4.70168 (  747)
  covalent geometry    : bond        0.00327 ( 6934)
  covalent geometry    : angle       0.63837 ( 9417)

*********************** 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
  138 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 SER cc_start: 0.7039 (m) cc_final: 0.6593 (t)
REVERT: B  350 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8438 (tttp)
REVERT: A  188 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.6074 (pt)
  outliers start: 18
  outliers final: 12
  residues processed: 133
  average time/residue: 0.1811
  time to fit residues: 32.5837
Evaluate side-chains
  125 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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  350 LYS
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   68 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 74 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 62 optimal weight:    0.1980
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 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**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.131890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.112647 restraints weight = 10081.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.116654 restraints weight = 5307.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.119399 restraints weight = 3414.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.5282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6934  Z= 0.138
  Angle     :  0.643  10.012   9417  Z= 0.315
  Chirality :  0.044   0.146   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 11.240 166.126    974
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.83 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.28), residues: 848
  helix: -0.35 (0.27), residues: 362
  sheet: -2.26 (0.44), residues: 130
  loop : -1.40 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP B 344 
 HIS   0.006   0.001   HIS B   6 
 PHE   0.030   0.002   PHE A 255 
 TYR   0.015   0.001   TYR A 103 
 ARG   0.007   0.001   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03205 (  245)
  hydrogen bonds       : angle       4.59188 (  747)
  covalent geometry    : bond        0.00328 ( 6934)
  covalent geometry    : angle       0.64300 ( 9417)

*********************** 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
  140 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 SER cc_start: 0.7227 (m) cc_final: 0.6747 (t)
REVERT: B  328 GLU cc_start: 0.7432 (pt0) cc_final: 0.7160 (mt-10)
REVERT: B  350 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8396 (tttp)
REVERT: A  182 VAL cc_start: 0.8300 (m) cc_final: 0.7840 (p)
REVERT: A  188 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6406 (pt)
REVERT: A  339 ARG cc_start: 0.7064 (mmp-170) cc_final: 0.6762 (mmp80)
  outliers start: 24
  outliers final: 15
  residues processed: 134
  average time/residue: 0.1782
  time to fit residues: 32.9003
Evaluate side-chains
  127 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
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  313 VAL
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  350 LYS
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  378 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
B 334 GLN
A  88 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.135842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.116638 restraints weight = 9910.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.120775 restraints weight = 5176.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.123567 restraints weight = 3304.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.5484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6934  Z= 0.113
  Angle     :  0.635   9.828   9417  Z= 0.307
  Chirality :  0.043   0.147   1027
  Planarity :  0.004   0.046   1224
  Dihedral  : 10.957 163.450    974
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.92 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.28), residues: 848
  helix: -0.19 (0.28), residues: 366
  sheet: -2.16 (0.44), residues: 130
  loop : -1.41 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 344 
 HIS   0.006   0.001   HIS B   6 
 PHE   0.026   0.002   PHE A 255 
 TYR   0.012   0.001   TYR A 103 
 ARG   0.007   0.001   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02995 (  245)
  hydrogen bonds       : angle       4.40784 (  747)
  covalent geometry    : bond        0.00266 ( 6934)
  covalent geometry    : angle       0.63452 ( 9417)

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

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  325 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7308 (mt-10)
REVERT: A  182 VAL cc_start: 0.8249 (m) cc_final: 0.7827 (p)
REVERT: A  188 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6573 (pt)
REVERT: A  214 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7863 (ttp80)
REVERT: A  326 LYS cc_start: 0.4730 (mttt) cc_final: 0.4497 (mttp)
REVERT: A  339 ARG cc_start: 0.7032 (mmp-170) cc_final: 0.6741 (mmp80)
REVERT: A  352 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7104 (mmtt)
  outliers start: 21
  outliers final: 14
  residues processed: 142
  average time/residue: 0.1776
  time to fit residues: 34.5543
Evaluate side-chains
  128 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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  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 54 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    0.4980
   chunk 13 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 227 HIS
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4035 r_free = 0.4035 target = 0.134079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.114313 restraints weight = 9979.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.118574 restraints weight = 5210.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.121422 restraints weight = 3331.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.5603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6934  Z= 0.142
  Angle     :  0.655  11.498   9417  Z= 0.319
  Chirality :  0.044   0.147   1027
  Planarity :  0.004   0.041   1224
  Dihedral  : 10.909 161.119    974
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.70 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.29), residues: 848
  helix: -0.16 (0.28), residues: 367
  sheet: -1.87 (0.44), residues: 132
  loop : -1.36 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 344 
 HIS   0.005   0.001   HIS B   6 
 PHE   0.026   0.002   PHE A 255 
 TYR   0.015   0.001   TYR A 103 
 ARG   0.006   0.001   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  245)
  hydrogen bonds       : angle       4.50412 (  747)
  covalent geometry    : bond        0.00335 ( 6934)
  covalent geometry    : angle       0.65518 ( 9417)

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

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  330 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7001 (mpp)
REVERT: A  182 VAL cc_start: 0.8324 (m) cc_final: 0.7910 (p)
REVERT: A  214 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7955 (tmm-80)
REVERT: A  326 LYS cc_start: 0.4751 (mttt) cc_final: 0.4539 (mttp)
REVERT: A  339 ARG cc_start: 0.7039 (mmp-170) cc_final: 0.6691 (mmp80)
REVERT: A  352 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7157 (mmtt)
  outliers start: 24
  outliers final: 15
  residues processed: 139
  average time/residue: 0.1837
  time to fit residues: 34.7729
Evaluate side-chains
  129 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
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  330 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  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 33 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 76 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.132401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.113298 restraints weight = 10149.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.117318 restraints weight = 5356.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.120121 restraints weight = 3438.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.5760

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= 0.134
  Angle     :  0.670  11.074   9417  Z= 0.327
  Chirality :  0.045   0.175   1027
  Planarity :  0.004   0.041   1224
  Dihedral  : 10.757 158.711    974
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.11 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.29), residues: 848
  helix: -0.11 (0.28), residues: 368
  sheet: -1.79 (0.44), residues: 132
  loop : -1.38 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP B 344 
 HIS   0.006   0.001   HIS B   6 
 PHE   0.025   0.002   PHE A 255 
 TYR   0.011   0.001   TYR A 357 
 ARG   0.007   0.001   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03209 (  245)
  hydrogen bonds       : angle       4.47691 (  747)
  covalent geometry    : bond        0.00316 ( 6934)
  covalent geometry    : angle       0.66963 ( 9417)

*********************** 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
  146 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  330 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7072 (mpp)
REVERT: A  182 VAL cc_start: 0.8274 (m) cc_final: 0.7881 (p)
REVERT: A  214 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7887 (tmm-80)
REVERT: A  326 LYS cc_start: 0.4779 (mttt) cc_final: 0.4475 (mttp)
REVERT: A  339 ARG cc_start: 0.7039 (mmp-170) cc_final: 0.6756 (mmp80)
REVERT: A  352 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7036 (mmtt)
  outliers start: 21
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1802
  time to fit residues: 34.0832
Evaluate side-chains
  136 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  297 LYS
Chi-restraints excluded: chain B residue  330 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  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 31 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    3.3188

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.124137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.104762 restraints weight = 10455.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.108659 restraints weight = 5505.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.111338 restraints weight = 3569.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.6011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   6934  Z= 0.245
  Angle     :  0.768  10.901   9417  Z= 0.386
  Chirality :  0.049   0.155   1027
  Planarity :  0.005   0.057   1224
  Dihedral  : 11.021 157.985    974
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.84 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.28), residues: 848
  helix: -0.39 (0.27), residues: 370
  sheet: -2.06 (0.43), residues: 130
  loop : -1.52 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP B 344 
 HIS   0.006   0.001   HIS B   6 
 PHE   0.026   0.002   PHE A 255 
 TYR   0.020   0.002   TYR A 103 
 ARG   0.009   0.001   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  245)
  hydrogen bonds       : angle       4.96337 (  747)
  covalent geometry    : bond        0.00575 ( 6934)
  covalent geometry    : angle       0.76797 ( 9417)

********************** 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
  142 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  330 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7378 (mpp)
REVERT: A    5 ILE cc_start: 0.8328 (pp) cc_final: 0.8011 (pt)
REVERT: A  182 VAL cc_start: 0.8678 (m) cc_final: 0.8285 (p)
REVERT: A  339 ARG cc_start: 0.7034 (mmp-170) cc_final: 0.6736 (mmp80)
REVERT: A  413 MET cc_start: 0.8095 (pmm) cc_final: 0.7887 (pmm)
  outliers start: 21
  outliers final: 16
  residues processed: 137
  average time/residue: 0.1662
  time to fit residues: 31.2020
Evaluate side-chains
  127 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
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  297 LYS
Chi-restraints excluded: chain B residue  330 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  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 67 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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
** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.132809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.113388 restraints weight = 10055.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.117564 restraints weight = 5285.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.120386 restraints weight = 3400.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.6098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6934  Z= 0.132
  Angle     :  0.697  11.154   9417  Z= 0.343
  Chirality :  0.045   0.162   1027
  Planarity :  0.004   0.042   1224
  Dihedral  : 10.580 160.450    974
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.97 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.29), residues: 848
  helix: -0.26 (0.27), residues: 373
  sheet: -1.90 (0.43), residues: 131
  loop : -1.42 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 344 
 HIS   0.007   0.001   HIS B   6 
 PHE   0.023   0.002   PHE A 255 
 TYR   0.012   0.001   TYR A 103 
 ARG   0.007   0.001   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03285 (  245)
  hydrogen bonds       : angle       4.71572 (  747)
  covalent geometry    : bond        0.00310 ( 6934)
  covalent geometry    : angle       0.69668 ( 9417)

===============================================================================
Job complete
usr+sys time: 2879.57 seconds
wall clock time: 50 minutes 41.54 seconds (3041.54 seconds total)