Starting phenix.real_space_refine
on Fri Feb 14 13:39:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rai_4776/02_2025/6rai_4776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rai_4776/02_2025/6rai_4776.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rai_4776/02_2025/6rai_4776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rai_4776/02_2025/6rai_4776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rai_4776/02_2025/6rai_4776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rai_4776/02_2025/6rai_4776.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      25      5.16       5
     C    6566      2.51       5
     N    1797      2.21       5
     O    1795      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10191
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4701
          Classifications: {'peptide': 587}
          Link IDs: {'PTRANS': 24, 'TRANS': 562}
    Chain: "B"
      Number of atoms: 4523
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4523
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 18, 'TRANS': 554}
    Chain: "C"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 897
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.09, per 1000 atoms: 0.60
  Number of scatterers: 10191
  At special positions: 0
  Unit cell: (103.392, 81.852, 156.165, 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      25     16.00
     P       6     15.00
     Mg      2     11.99
     O    1795      8.00
     N    1797      7.00
     C    6566      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 108 " distance=2.06

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2342

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 6 sheets defined
      64.9% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 23
      removed outlier: 3.874A  pdb=" N   ARG A  20 " --> pdb=" O   ALA A  16 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   TYR A  21 " --> pdb=" O   ARG A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 28
      removed outlier: 5.441A  pdb=" N   LEU A  27 " --> pdb=" O   PRO A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 45
    Processing helix  chain 'A' and resid 46 through 55
      removed outlier: 4.239A  pdb=" N   PHE A  50 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 120
      removed outlier: 3.560A  pdb=" N   ARG A  69 " --> pdb=" O   PRO A  65 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   PHE A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU A  74 " --> pdb=" O   PHE A  70 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   TRP A  75 " --> pdb=" O   HIS A  71 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
    Processing helix  chain 'A' and resid 129 through 149
      removed outlier: 3.683A  pdb=" N   ARG A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASP A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   VAL A 141 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ILE A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 173
      removed outlier: 3.936A  pdb=" N   PHE A 160 " --> pdb=" O   ILE A 156 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 3.903A  pdb=" N   VAL A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 222
      removed outlier: 3.894A  pdb=" N   SER A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ARG A 203 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 229
    Processing helix  chain 'A' and resid 231 through 285
      removed outlier: 3.526A  pdb=" N   GLU A 236 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   TRP A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   LEU A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE A 260 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   PHE A 261 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.585A  pdb=" N   ASP A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLY A 281 " --> pdb=" O   TYR A 277 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL A 283 " --> pdb=" O   GLY A 279 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
    Processing helix  chain 'A' and resid 304 through 313
    Processing helix  chain 'A' and resid 313 through 332
      removed outlier: 3.543A  pdb=" N   PHE A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 407
      removed outlier: 3.545A  pdb=" N   VAL A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 435
      removed outlier: 3.586A  pdb=" N   HIS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 455
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.543A  pdb=" N   VAL A 466 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 481
    Processing helix  chain 'A' and resid 484 through 488
    Processing helix  chain 'A' and resid 498 through 512
    Processing helix  chain 'A' and resid 529 through 544
      removed outlier: 3.684A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 586
    Processing helix  chain 'A' and resid 586 through 597
      removed outlier: 3.658A  pdb=" N   ALA A 591 " --> pdb=" O   GLY A 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 18
      Proline residue:  B  15  - end of helix
    Processing helix  chain 'B' and resid 20 through 39
    Processing helix  chain 'B' and resid 40 through 53
    Processing helix  chain 'B' and resid 57 through 103
      removed outlier: 4.485A  pdb=" N   TYR B  61 " --> pdb=" O   GLY B  57 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA B  62 " --> pdb=" O   PHE B  58 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 112
      removed outlier: 3.680A  pdb=" N   LYS B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 124
      removed outlier: 3.528A  pdb=" N   ASN B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 133
    Processing helix  chain 'B' and resid 134 through 156
    Processing helix  chain 'B' and resid 158 through 167
    Processing helix  chain 'B' and resid 168 through 207
      removed outlier: 4.254A  pdb=" N   ALA B 175 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG B 177 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   PHE B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG B 185 " --> pdb=" O   ARG B 181 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU B 192 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL B 193 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 214
      removed outlier: 3.627A  pdb=" N   VAL B 211 " --> pdb=" O   GLY B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 243
      removed outlier: 3.709A  pdb=" N   LEU B 227 " --> pdb=" O   TRP B 223 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU B 233 " --> pdb=" O   ARG B 229 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 238 " --> pdb=" O   LYS B 234 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 270
      removed outlier: 3.866A  pdb=" N   GLY B 250 " --> pdb=" O   HIS B 246 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   MET B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG B 270 " --> pdb=" O   ALA B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 294
      removed outlier: 4.434A  pdb=" N   TRP B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      Proline residue:  B 291  - end of helix
      removed outlier: 3.646A  pdb=" N   GLY B 294 " --> pdb=" O   TRP B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 317
      removed outlier: 3.773A  pdb=" N   LEU B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.834A  pdb=" N   LEU B 335 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 383
    Processing helix  chain 'B' and resid 406 through 413
      removed outlier: 3.640A  pdb=" N   LYS B 412 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 433
    Processing helix  chain 'B' and resid 440 through 451
    Processing helix  chain 'B' and resid 453 through 458
    Processing helix  chain 'B' and resid 462 through 466
      removed outlier: 3.562A  pdb=" N   GLU B 465 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 473
      removed outlier: 3.822A  pdb=" N   ILE B 473 " --> pdb=" O   GLU B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 491
      removed outlier: 4.229A  pdb=" N   LYS B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 520
      removed outlier: 3.888A  pdb=" N   THR B 519 " --> pdb=" O   GLN B 515 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL B 520 " --> pdb=" O   GLY B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 537
    Processing helix  chain 'B' and resid 555 through 561
      removed outlier: 3.731A  pdb=" N   GLN B 561 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 575
      removed outlier: 3.885A  pdb=" N   ALA B 567 " --> pdb=" O   GLY B 563 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.925A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 382
      removed outlier: 6.256A  pdb=" N   LEU A 360 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   LYS A 377 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL A 358 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   VAL A 379 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ARG A 356 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   PHE A 381 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   GLU A 354 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   PHE A 355 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   PHE A 418 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ASP A 357 " --> pdb=" O   CYS A 416 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   CYS A 416 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG A 414 " --> pdb=" O   TRP A 359 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 6.508A  pdb=" N   LYS A 388 " --> pdb=" O   ARG A 564 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   LEU A 566 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ALA A 390 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL A 392 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU A 575 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361
      removed outlier: 6.553A  pdb=" N   LEU B 353 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   LYS B 347 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ARG B 355 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   GLY B 345 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   LEU B 357 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   GLU B 392 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.370A  pdb=" N   GLY B 415 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   ASP B 499 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ALA B 417 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   THR B 366 " --> pdb=" O   TRP B 541 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   ILE B 543 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   GLY B 368 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   LEU B 545 " --> pdb=" O   GLY B 368 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   THR B 370 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU B 552 " --> pdb=" O   VAL B 544 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASP B 546 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   ILE B 550 " --> pdb=" O   ASP B 546 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.660A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.529A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    605 hydrogen bonds defined for protein.
    1770 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.51

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1610
        1.31 -     1.43: 2806
        1.43 -     1.56: 5915
        1.56 -     1.69: 22
        1.69 -     1.81: 45
  Bond restraints: 10398
  Sorted by residual:
  bond pdb=" C4  ATP B 601 "
       pdb=" C5  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.87e+01
  bond pdb=" C4  ATP A 701 "
       pdb=" C5  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.460 -0.072 1.00e-02 1.00e+04 5.21e+01
  bond pdb=" N   PRO B 320 "
       pdb=" CD  PRO B 320 "
    ideal  model  delta    sigma   weight residual
    1.473  1.562 -0.089 1.40e-02 5.10e+03 4.08e+01
  bond pdb=" N   PRO A 443 "
       pdb=" CD  PRO A 443 "
    ideal  model  delta    sigma   weight residual
    1.473  1.561 -0.088 1.40e-02 5.10e+03 3.95e+01
  bond pdb=" C5  ATP A 701 "
       pdb=" C6  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.471 -0.062 1.00e-02 1.00e+04 3.87e+01
  ... (remaining 10393 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 13708
        3.75 -     7.50: 353
        7.50 -    11.25: 44
       11.25 -    15.00: 0
       15.00 -    18.76: 3
  Bond angle restraints: 14108
  Sorted by residual:
  angle pdb=" PB  ATP A 701 "
        pdb=" O3B ATP A 701 "
        pdb=" PG  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     139.87  121.11   18.76 1.00e+00 1.00e+00 3.52e+02
  angle pdb=" PB  ATP B 601 "
        pdb=" O3B ATP B 601 "
        pdb=" PG  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     139.87  122.72   17.15 1.00e+00 1.00e+00 2.94e+02
  angle pdb=" PA  ATP B 601 "
        pdb=" O3A ATP B 601 "
        pdb=" PB  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     136.83  120.35   16.48 1.00e+00 1.00e+00 2.72e+02
  angle pdb=" PA  ATP A 701 "
        pdb=" O3A ATP A 701 "
        pdb=" PB  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     136.83  128.10    8.73 1.00e+00 1.00e+00 7.62e+01
  angle pdb=" N   LEU B  45 "
        pdb=" CA  LEU B  45 "
        pdb=" C   LEU B  45 "
      ideal   model   delta    sigma   weight residual
     111.28  120.38   -9.10 1.09e+00 8.42e-01 6.97e+01
  ... (remaining 14103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 5925
       17.37 -    34.75: 220
       34.75 -    52.12: 44
       52.12 -    69.49: 9
       69.49 -    86.86: 9
  Dihedral angle restraints: 6207
    sinusoidal: 2547
      harmonic: 3660
  Sorted by residual:
  dihedral pdb=" C   HIS A 579 "
           pdb=" N   HIS A 579 "
           pdb=" CA  HIS A 579 "
           pdb=" CB  HIS A 579 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.97   16.37     0      2.50e+00 1.60e-01 4.29e+01
  dihedral pdb=" N   HIS A 579 "
           pdb=" C   HIS A 579 "
           pdb=" CA  HIS A 579 "
           pdb=" CB  HIS A 579 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.97  -13.17     0      2.50e+00 1.60e-01 2.78e+01
  dihedral pdb=" C   ARG A 560 "
           pdb=" N   ARG A 560 "
           pdb=" CA  ARG A 560 "
           pdb=" CB  ARG A 560 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.25   11.65     0      2.50e+00 1.60e-01 2.17e+01
  ... (remaining 6204 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1374
       0.108 -    0.216: 191
       0.216 -    0.325: 29
       0.325 -    0.433: 9
       0.433 -    0.541: 3
  Chirality restraints: 1606
  Sorted by residual:
  chirality pdb=" CA  HIS A 579 "
            pdb=" N   HIS A 579 "
            pdb=" C   HIS A 579 "
            pdb=" CB  HIS A 579 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.32e+00
  chirality pdb=" CA  VAL C 109 "
            pdb=" N   VAL C 109 "
            pdb=" C   VAL C 109 "
            pdb=" CB  VAL C 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.88   -0.44 2.00e-01 2.50e+01 4.80e+00
  chirality pdb=" CA  LEU C 104 "
            pdb=" N   LEU C 104 "
            pdb=" C   LEU C 104 "
            pdb=" CB  LEU C 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.79e+00
  ... (remaining 1603 not shown)

  Planarity restraints: 1783
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 231 "    0.019 2.00e-02 2.50e+03   3.78e-02 1.43e+01
        pdb=" C   LYS A 231 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LYS A 231 "    0.025 2.00e-02 2.50e+03
        pdb=" N   GLU A 232 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 154 "   -0.017 2.00e-02 2.50e+03   3.29e-02 1.09e+01
        pdb=" C   GLY A 154 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLY A 154 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   VAL A 155 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 287 "   -0.014 2.00e-02 2.50e+03   2.93e-02 8.59e+00
        pdb=" C   ALA A 287 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ALA A 287 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL A 288 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1780 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 53
        2.54 -     3.13: 7245
        3.13 -     3.72: 15497
        3.72 -     4.31: 22725
        4.31 -     4.90: 38148
  Nonbonded interactions: 83668
  Sorted by model distance:
  nonbonded pdb="MG    MG A 702 "
            pdb=" O   HOH A 802 "
     model   vdw
     1.948 2.170
  nonbonded pdb="MG    MG A 702 "
            pdb=" O   HOH A 801 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" OG  SER B 378 "
            pdb="MG    MG B 602 "
     model   vdw
     2.094 2.170
  nonbonded pdb="MG    MG B 602 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.109 2.170
  nonbonded pdb=" OG1 THR A 400 "
            pdb="MG    MG A 702 "
     model   vdw
     2.114 2.170
  ... (remaining 83663 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     24.810
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.089  10398  Z= 0.571
  Angle     :  1.397  18.755  14108  Z= 0.971
  Chirality :  0.083   0.541   1606
  Planarity :  0.008   0.056   1783
  Dihedral  : 10.559  86.864   3859
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.51 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.19), residues: 1275
  helix: -2.17 (0.15), residues: 756
  sheet:  0.02 (0.47), residues: 120
  loop : -2.43 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  22 
 HIS   0.006   0.001   HIS A 121 
 PHE   0.039   0.003   PHE A 304 
 TYR   0.028   0.003   TYR B 284 
 ARG   0.006   0.001   ARG B 240 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 1.189 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8211 (tp) cc_final: 0.7975 (tp)
REVERT: A   58 LEU cc_start: 0.8143 (mt) cc_final: 0.7859 (mp)
REVERT: A   96 TYR cc_start: 0.8440 (t80) cc_final: 0.7886 (t80)
REVERT: A  145 ASN cc_start: 0.8889 (t0) cc_final: 0.8658 (t0)
REVERT: A  168 PHE cc_start: 0.8304 (t80) cc_final: 0.8080 (t80)
REVERT: A  206 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7685 (mpt180)
REVERT: A  238 LYS cc_start: 0.8330 (mttt) cc_final: 0.7798 (mttp)
REVERT: A  357 ASP cc_start: 0.7979 (t70) cc_final: 0.7552 (t0)
REVERT: A  388 LYS cc_start: 0.7429 (mttt) cc_final: 0.6849 (mttm)
REVERT: A  425 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7324 (mtm-85)
REVERT: A  431 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7484 (mp0)
REVERT: A  536 LEU cc_start: 0.8038 (pp) cc_final: 0.7705 (mp)
REVERT: A  555 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7619 (mtt180)
REVERT: B  131 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6999 (mm-30)
REVERT: B  299 MET cc_start: 0.7514 (mmt) cc_final: 0.6947 (mmt)
REVERT: B  510 GLU cc_start: 0.6683 (tt0) cc_final: 0.6441 (pp20)
REVERT: B  532 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6947 (mmm160)
REVERT: C   39 GLN cc_start: 0.7757 (tt0) cc_final: 0.7403 (tp40)
REVERT: C   65 LYS cc_start: 0.7938 (ptmm) cc_final: 0.7712 (pttt)
REVERT: C   98 THR cc_start: 0.7947 (m) cc_final: 0.7552 (p)
  outliers start: 0
  outliers final: 1
  residues processed: 271
  average time/residue: 1.8010
  time to fit residues: 513.9627
Evaluate side-chains
  167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0030
   chunk 53 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0980
   chunk 38 optimal weight:    0.0980
   chunk 60 optimal weight:    0.6980
   chunk 74 optimal weight:    0.3980
   chunk 115 optimal weight:    0.3980
   overall best weight:    0.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
A 103 GLN
A 146 GLN
A 302 GLN
A 305 GLN
A 308 GLN
A 318 GLN
A 429 GLN
A 503 GLN
A 537 GLN
B 111 HIS
B 113 HIS
B 191 GLN
B 431 ASN
B 538 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.146677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.120080 restraints weight = 11697.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.83
r_work: 0.3221 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10398  Z= 0.158
  Angle     :  0.578   7.607  14108  Z= 0.298
  Chirality :  0.040   0.164   1606
  Planarity :  0.005   0.040   1783
  Dihedral  :  7.476  75.781   1506
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.45 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.22), residues: 1275
  helix: -0.26 (0.18), residues: 783
  sheet:  0.29 (0.47), residues: 124
  loop : -1.81 (0.27), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C  36 
 HIS   0.004   0.001   HIS B 111 
 PHE   0.013   0.001   PHE A 304 
 TYR   0.025   0.001   TYR A 589 
 ARG   0.007   0.001   ARG A 195 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 208
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.8649 (m-80) cc_final: 0.8381 (m-80)
REVERT: A   33 LEU cc_start: 0.8586 (mp) cc_final: 0.8254 (mm)
REVERT: A   41 LEU cc_start: 0.8289 (mt) cc_final: 0.7958 (mt)
REVERT: A   96 TYR cc_start: 0.8570 (t80) cc_final: 0.8193 (t80)
REVERT: A  104 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7889 (mtp-110)
REVERT: A  146 GLN cc_start: 0.8085 (mp-120) cc_final: 0.7793 (mp-120)
REVERT: A  206 ARG cc_start: 0.8296 (mmt180) cc_final: 0.7958 (mpt180)
REVERT: A  334 GLU cc_start: 0.8189 (tt0) cc_final: 0.7833 (tm-30)
REVERT: A  354 GLU cc_start: 0.8039 (tt0) cc_final: 0.7811 (tm-30)
REVERT: A  357 ASP cc_start: 0.8504 (t70) cc_final: 0.8168 (t70)
REVERT: A  425 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7716 (mtt90)
REVERT: A  431 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7847 (mp0)
REVERT: A  467 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7640 (mp0)
REVERT: B  120 ASN cc_start: 0.8860 (t0) cc_final: 0.8537 (t0)
REVERT: B  209 ARG cc_start: 0.8335 (mpt-90) cc_final: 0.8130 (mpt-90)
REVERT: B  219 ARG cc_start: 0.8295 (mtp85) cc_final: 0.8006 (tpp80)
REVERT: B  255 PHE cc_start: 0.7851 (t80) cc_final: 0.7480 (m-80)
REVERT: B  299 MET cc_start: 0.8459 (mmt) cc_final: 0.7862 (mmp)
REVERT: B  342 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8136 (mm-30)
REVERT: B  494 LYS cc_start: 0.8715 (mmtm) cc_final: 0.8471 (mttm)
REVERT: B  510 GLU cc_start: 0.7063 (tt0) cc_final: 0.6374 (pp20)
REVERT: B  515 GLN cc_start: 0.7995 (mt0) cc_final: 0.7602 (mm-40)
REVERT: B  532 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7597 (mmm160)
REVERT: B  549 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7996 (mtt180)
REVERT: B  552 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8273 (mt-10)
REVERT: C   39 GLN cc_start: 0.7790 (tt0) cc_final: 0.7278 (tp40)
REVERT: C   65 LYS cc_start: 0.7913 (ptmm) cc_final: 0.7629 (ptpt)
REVERT: C   82 GLN cc_start: 0.6723 (tp40) cc_final: 0.6301 (tp40)
REVERT: C   83 MET cc_start: 0.7186 (mtm) cc_final: 0.6664 (mpp)
REVERT: C   98 THR cc_start: 0.8379 (m) cc_final: 0.8142 (p)
  outliers start: 18
  outliers final: 5
  residues processed: 221
  average time/residue: 1.5969
  time to fit residues: 373.5854
Evaluate side-chains
  171 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 164
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  377 LYS
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  342 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 111 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 125 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
A 429 GLN
B  53 GLN
B 111 HIS
B 113 HIS
C  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.138420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.111392 restraints weight = 12021.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.82
r_work: 0.3081 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10398  Z= 0.249
  Angle     :  0.586   7.110  14108  Z= 0.297
  Chirality :  0.041   0.169   1606
  Planarity :  0.004   0.045   1783
  Dihedral  :  6.922  78.310   1504
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.12 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.23), residues: 1275
  helix:  0.47 (0.18), residues: 784
  sheet:  0.30 (0.46), residues: 124
  loop : -1.39 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  22 
 HIS   0.004   0.001   HIS B 111 
 PHE   0.018   0.001   PHE A 304 
 TYR   0.020   0.001   TYR A 588 
 ARG   0.009   0.001   ARG B 218 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7427 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8454 (mp) cc_final: 0.8151 (mm)
REVERT: A  134 MET cc_start: 0.8250 (mmm) cc_final: 0.7919 (mmm)
REVERT: A  146 GLN cc_start: 0.8333 (mp-120) cc_final: 0.8117 (mp-120)
REVERT: A  175 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8264 (tppp)
REVERT: A  234 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7586 (mp0)
REVERT: A  245 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7661 (t0)
REVERT: A  255 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7841 (ttp-110)
REVERT: A  309 ASP cc_start: 0.8182 (t70) cc_final: 0.7960 (t70)
REVERT: A  334 GLU cc_start: 0.8294 (tt0) cc_final: 0.7922 (tm-30)
REVERT: A  354 GLU cc_start: 0.8142 (tt0) cc_final: 0.7916 (tm-30)
REVERT: A  357 ASP cc_start: 0.8549 (t70) cc_final: 0.8324 (t70)
REVERT: A  423 ASP cc_start: 0.8060 (m-30) cc_final: 0.7844 (t70)
REVERT: A  425 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7741 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7995 (mp0)
REVERT: A  593 TYR cc_start: 0.7400 (t80) cc_final: 0.7171 (t80)
REVERT: B   63 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8258 (tp)
REVERT: B  219 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8075 (tpp80)
REVERT: B  255 PHE cc_start: 0.8038 (t80) cc_final: 0.7653 (m-80)
REVERT: B  510 GLU cc_start: 0.7128 (tt0) cc_final: 0.6425 (pp20)
REVERT: B  532 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7652 (mmm160)
REVERT: B  549 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8083 (mtt180)
REVERT: B  568 GLU cc_start: 0.7644 (tt0) cc_final: 0.7303 (tp30)
REVERT: B  574 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7222 (ttpt)
REVERT: C   39 GLN cc_start: 0.7840 (tt0) cc_final: 0.7261 (tp40)
REVERT: C   65 LYS cc_start: 0.7968 (ptmm) cc_final: 0.7706 (pttt)
REVERT: C   82 GLN cc_start: 0.6753 (tp40) cc_final: 0.6281 (tp40)
REVERT: C   98 THR cc_start: 0.8143 (m) cc_final: 0.7842 (p)
  outliers start: 29
  outliers final: 10
  residues processed: 187
  average time/residue: 1.6083
  time to fit residues: 319.5537
Evaluate side-chains
  163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  505 VAL
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 117 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0030
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
B  53 GLN
B 120 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.139544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.113086 restraints weight = 11956.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.78
r_work: 0.3108 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10398  Z= 0.182
  Angle     :  0.527   7.273  14108  Z= 0.268
  Chirality :  0.040   0.182   1606
  Planarity :  0.004   0.040   1783
  Dihedral  :  6.655  86.811   1504
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.65 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.23), residues: 1275
  helix:  0.92 (0.19), residues: 784
  sheet:  0.46 (0.48), residues: 114
  loop : -1.14 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  36 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.021   0.001   PHE A 171 
 TYR   0.018   0.001   TYR A 588 
 ARG   0.006   0.000   ARG A 594 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7400 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8455 (mp) cc_final: 0.8175 (mm)
REVERT: A  134 MET cc_start: 0.8183 (mmm) cc_final: 0.7788 (mmm)
REVERT: A  146 GLN cc_start: 0.8270 (mp-120) cc_final: 0.7923 (mp-120)
REVERT: A  175 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8172 (tppp)
REVERT: A  234 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7733 (mp0)
REVERT: A  245 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7609 (t0)
REVERT: A  309 ASP cc_start: 0.8209 (t70) cc_final: 0.7958 (t70)
REVERT: A  334 GLU cc_start: 0.8264 (tt0) cc_final: 0.7952 (tm-30)
REVERT: A  354 GLU cc_start: 0.8132 (tt0) cc_final: 0.7914 (tm-30)
REVERT: A  357 ASP cc_start: 0.8530 (t70) cc_final: 0.8179 (t70)
REVERT: A  423 ASP cc_start: 0.8163 (m-30) cc_final: 0.7863 (t70)
REVERT: A  425 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7768 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7986 (mp0)
REVERT: A  541 TYR cc_start: 0.7182 (m-10) cc_final: 0.6937 (t80)
REVERT: B   63 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8241 (tp)
REVERT: B  120 ASN cc_start: 0.8969 (t0) cc_final: 0.8508 (t0)
REVERT: B  131 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7965 (mm-30)
REVERT: B  173 PHE cc_start: 0.7319 (t80) cc_final: 0.6825 (m-80)
REVERT: B  181 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7640 (tpp80)
REVERT: B  219 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8060 (tpp80)
REVERT: B  255 PHE cc_start: 0.8053 (t80) cc_final: 0.7632 (m-80)
REVERT: B  401 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7349 (tm-30)
REVERT: B  426 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7943 (mm-30)
REVERT: B  510 GLU cc_start: 0.7148 (tt0) cc_final: 0.6411 (pp20)
REVERT: B  515 GLN cc_start: 0.8010 (mt0) cc_final: 0.7644 (mm-40)
REVERT: B  532 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7612 (mmm160)
REVERT: B  568 GLU cc_start: 0.7553 (tt0) cc_final: 0.7254 (tp30)
REVERT: C   18 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6189 (tt)
REVERT: C   39 GLN cc_start: 0.7873 (tt0) cc_final: 0.7383 (tp40)
REVERT: C   65 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7696 (pttt)
REVERT: C   82 GLN cc_start: 0.6882 (tp40) cc_final: 0.6414 (tp40)
REVERT: C   98 THR cc_start: 0.8168 (m) cc_final: 0.7857 (p)
  outliers start: 26
  outliers final: 6
  residues processed: 190
  average time/residue: 1.4829
  time to fit residues: 299.8835
Evaluate side-chains
  177 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 166
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain C residue   18 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 114 optimal weight:    0.6980
   chunk 116 optimal weight:    9.9990
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 126 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
B  53 GLN
** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.137806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.111299 restraints weight = 12022.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.79
r_work: 0.3067 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10398  Z= 0.206
  Angle     :  0.536   7.676  14108  Z= 0.271
  Chirality :  0.040   0.168   1606
  Planarity :  0.004   0.039   1783
  Dihedral  :  6.664  86.503   1504
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.94 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.23), residues: 1275
  helix:  1.12 (0.19), residues: 784
  sheet:  0.39 (0.47), residues: 114
  loop : -0.98 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  36 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.015   0.001   PHE A 304 
 TYR   0.016   0.001   TYR A 588 
 ARG   0.009   0.000   ARG B 218 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 171
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7405 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8513 (mp) cc_final: 0.8238 (mm)
REVERT: A   64 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6257 (pmt-80)
REVERT: A  134 MET cc_start: 0.8242 (mmm) cc_final: 0.7875 (mmm)
REVERT: A  146 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8022 (mp-120)
REVERT: A  232 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7070 (mp0)
REVERT: A  234 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7801 (mp0)
REVERT: A  245 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7675 (t0)
REVERT: A  255 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7808 (ttp-110)
REVERT: A  309 ASP cc_start: 0.8229 (t70) cc_final: 0.7974 (t70)
REVERT: A  334 GLU cc_start: 0.8352 (tt0) cc_final: 0.7979 (tm-30)
REVERT: A  354 GLU cc_start: 0.8162 (tt0) cc_final: 0.7961 (tm-30)
REVERT: A  357 ASP cc_start: 0.8546 (t70) cc_final: 0.8220 (t70)
REVERT: A  423 ASP cc_start: 0.8203 (m-30) cc_final: 0.7913 (t70)
REVERT: A  425 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7837 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7995 (mp0)
REVERT: A  541 TYR cc_start: 0.7236 (m-10) cc_final: 0.6955 (t80)
REVERT: B   63 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8319 (tp)
REVERT: B  131 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8008 (mm-30)
REVERT: B  173 PHE cc_start: 0.7418 (t80) cc_final: 0.6987 (m-80)
REVERT: B  181 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7682 (tpp80)
REVERT: B  219 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8078 (tpp80)
REVERT: B  255 PHE cc_start: 0.8121 (t80) cc_final: 0.7719 (m-80)
REVERT: B  401 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7370 (tm-30)
REVERT: B  426 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7965 (mm-30)
REVERT: B  510 GLU cc_start: 0.7194 (tt0) cc_final: 0.6503 (pp20)
REVERT: B  515 GLN cc_start: 0.8022 (mt0) cc_final: 0.7693 (mm-40)
REVERT: B  532 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7654 (mmm160)
REVERT: B  574 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7347 (pttp)
REVERT: C   39 GLN cc_start: 0.8003 (tt0) cc_final: 0.7356 (tp40)
REVERT: C   65 LYS cc_start: 0.7967 (ptmm) cc_final: 0.7708 (pttt)
REVERT: C   82 GLN cc_start: 0.6881 (tp40) cc_final: 0.6476 (tp40)
REVERT: C   98 THR cc_start: 0.8223 (m) cc_final: 0.7913 (p)
  outliers start: 30
  outliers final: 9
  residues processed: 189
  average time/residue: 1.5317
  time to fit residues: 307.3267
Evaluate side-chains
  176 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 ARG
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 106 optimal weight:    0.3980
   chunk 52 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.110945 restraints weight = 12034.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.82
r_work: 0.3099 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10398  Z= 0.198
  Angle     :  0.534   8.352  14108  Z= 0.269
  Chirality :  0.040   0.170   1606
  Planarity :  0.004   0.038   1783
  Dihedral  :  6.613  84.116   1504
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.84 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.23), residues: 1275
  helix:  1.27 (0.19), residues: 784
  sheet:  0.48 (0.48), residues: 114
  loop : -0.87 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP C  36 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.025   0.001   PHE A 171 
 TYR   0.015   0.001   TYR A 588 
 ARG   0.006   0.000   ARG B 218 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7448 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8400 (mp) cc_final: 0.8133 (mm)
REVERT: A   64 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6085 (pmt-80)
REVERT: A   68 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5582 (pt0)
REVERT: A  134 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7819 (mmm)
REVERT: A  146 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7906 (mp-120)
REVERT: A  218 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8167 (tt0)
REVERT: A  232 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6955 (mp0)
REVERT: A  234 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7744 (mp0)
REVERT: A  245 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7694 (t0)
REVERT: A  309 ASP cc_start: 0.8217 (t70) cc_final: 0.7977 (t70)
REVERT: A  334 GLU cc_start: 0.8341 (tt0) cc_final: 0.7964 (tm-30)
REVERT: A  354 GLU cc_start: 0.8151 (tt0) cc_final: 0.7919 (tm-30)
REVERT: A  357 ASP cc_start: 0.8496 (t70) cc_final: 0.8151 (t70)
REVERT: A  423 ASP cc_start: 0.8207 (m-30) cc_final: 0.7884 (t70)
REVERT: A  425 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7769 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7893 (mp0)
REVERT: A  537 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7767 (mt0)
REVERT: A  541 TYR cc_start: 0.7232 (m-10) cc_final: 0.6861 (t80)
REVERT: B   63 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (tp)
REVERT: B  120 ASN cc_start: 0.8977 (t0) cc_final: 0.8488 (t0)
REVERT: B  131 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7986 (mm-30)
REVERT: B  173 PHE cc_start: 0.7236 (t80) cc_final: 0.6767 (m-80)
REVERT: B  181 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7644 (tpp80)
REVERT: B  219 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8062 (tpp80)
REVERT: B  255 PHE cc_start: 0.8068 (t80) cc_final: 0.7642 (m-80)
REVERT: B  401 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7255 (tm-30)
REVERT: B  426 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7942 (mm-30)
REVERT: B  510 GLU cc_start: 0.7172 (tt0) cc_final: 0.6407 (pp20)
REVERT: B  515 GLN cc_start: 0.8051 (mt0) cc_final: 0.7652 (mm-40)
REVERT: B  532 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7553 (mmm160)
REVERT: B  574 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7266 (pttp)
REVERT: C   39 GLN cc_start: 0.7985 (tt0) cc_final: 0.7364 (tp40)
REVERT: C   65 LYS cc_start: 0.7914 (ptmm) cc_final: 0.7627 (pttt)
REVERT: C   82 GLN cc_start: 0.6849 (tp40) cc_final: 0.6434 (tp40)
REVERT: C   98 THR cc_start: 0.8097 (m) cc_final: 0.7748 (p)
  outliers start: 31
  outliers final: 12
  residues processed: 188
  average time/residue: 1.5732
  time to fit residues: 313.5578
Evaluate side-chains
  182 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 ARG
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 63 optimal weight:    0.4980
   chunk 51 optimal weight:    0.3980
   chunk 109 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.137880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.111087 restraints weight = 12121.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.83
r_work: 0.3097 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10398  Z= 0.192
  Angle     :  0.534   8.197  14108  Z= 0.268
  Chirality :  0.040   0.171   1606
  Planarity :  0.003   0.038   1783
  Dihedral  :  6.572  83.313   1504
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.13 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.23), residues: 1275
  helix:  1.38 (0.19), residues: 784
  sheet:  0.51 (0.49), residues: 115
  loop : -0.80 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP C  36 
 HIS   0.002   0.001   HIS B 454 
 PHE   0.015   0.001   PHE A 304 
 TYR   0.015   0.001   TYR B 164 
 ARG   0.005   0.000   ARG A 255 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.7839 (mt) cc_final: 0.7450 (tt)
REVERT: A   20 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7462 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8411 (mp) cc_final: 0.8141 (mm)
REVERT: A   64 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6088 (pmt-80)
REVERT: A   96 TYR cc_start: 0.8642 (t80) cc_final: 0.8439 (t80)
REVERT: A  134 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7809 (mmm)
REVERT: A  146 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7892 (mp-120)
REVERT: A  232 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6958 (mp0)
REVERT: A  245 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7747 (t0)
REVERT: A  255 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7815 (ttp-110)
REVERT: A  309 ASP cc_start: 0.8208 (t70) cc_final: 0.7961 (t70)
REVERT: A  334 GLU cc_start: 0.8339 (tt0) cc_final: 0.7963 (tm-30)
REVERT: A  354 GLU cc_start: 0.8159 (tt0) cc_final: 0.7933 (tm-30)
REVERT: A  357 ASP cc_start: 0.8485 (t70) cc_final: 0.8136 (t70)
REVERT: A  423 ASP cc_start: 0.8198 (m-30) cc_final: 0.7893 (t70)
REVERT: A  425 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7765 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7894 (mp0)
REVERT: A  537 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7729 (mt0)
REVERT: A  541 TYR cc_start: 0.7224 (m-10) cc_final: 0.6844 (t80)
REVERT: B   63 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8268 (tp)
REVERT: B  119 MET cc_start: 0.8728 (mmm) cc_final: 0.8476 (mmm)
REVERT: B  131 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7955 (mm-30)
REVERT: B  173 PHE cc_start: 0.7225 (t80) cc_final: 0.6711 (m-80)
REVERT: B  181 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7647 (tpp80)
REVERT: B  218 ARG cc_start: 0.8358 (mtp85) cc_final: 0.8111 (mtm110)
REVERT: B  219 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7978 (tpp80)
REVERT: B  255 PHE cc_start: 0.8089 (t80) cc_final: 0.7666 (m-80)
REVERT: B  401 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7235 (tm-30)
REVERT: B  426 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7973 (mm-30)
REVERT: B  510 GLU cc_start: 0.7169 (tt0) cc_final: 0.6405 (pp20)
REVERT: B  515 GLN cc_start: 0.8056 (mt0) cc_final: 0.7661 (mm-40)
REVERT: B  532 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7588 (mmm160)
REVERT: B  557 GLU cc_start: 0.8013 (mp0) cc_final: 0.7813 (mp0)
REVERT: B  574 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7248 (pttp)
REVERT: C   18 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.5899 (tm)
REVERT: C   39 GLN cc_start: 0.8013 (tt0) cc_final: 0.7421 (tp40)
REVERT: C   65 LYS cc_start: 0.7923 (ptmm) cc_final: 0.7616 (pttm)
REVERT: C   82 GLN cc_start: 0.6723 (tp40) cc_final: 0.6347 (tp40)
REVERT: C   98 THR cc_start: 0.8019 (m) cc_final: 0.7658 (p)
  outliers start: 30
  outliers final: 9
  residues processed: 179
  average time/residue: 1.6012
  time to fit residues: 304.3932
Evaluate side-chains
  174 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 ARG
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 95 optimal weight:    0.4980
   chunk 112 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 HIS
B  53 GLN
B 120 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.110208 restraints weight = 11940.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.82
r_work: 0.3116 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10398  Z= 0.206
  Angle     :  0.544   8.705  14108  Z= 0.272
  Chirality :  0.040   0.170   1606
  Planarity :  0.004   0.036   1783
  Dihedral  :  6.633  82.703   1504
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.74 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.23), residues: 1275
  helix:  1.41 (0.19), residues: 786
  sheet:  0.44 (0.48), residues: 115
  loop : -0.81 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP C  36 
 HIS   0.002   0.001   HIS B 454 
 PHE   0.026   0.001   PHE A 171 
 TYR   0.015   0.001   TYR B 164 
 ARG   0.004   0.000   ARG A 255 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7868 (mt) cc_final: 0.7499 (tt)
REVERT: A   20 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7508 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8453 (mp) cc_final: 0.8186 (mm)
REVERT: A   64 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6241 (pmt-80)
REVERT: A   96 TYR cc_start: 0.8629 (t80) cc_final: 0.8427 (t80)
REVERT: A  134 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7850 (mmm)
REVERT: A  146 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7912 (mp-120)
REVERT: A  166 LEU cc_start: 0.7504 (tp) cc_final: 0.7275 (tm)
REVERT: A  218 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8188 (tt0)
REVERT: A  232 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6924 (mp0)
REVERT: A  245 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7757 (t0)
REVERT: A  255 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7883 (ttp-110)
REVERT: A  309 ASP cc_start: 0.8235 (t70) cc_final: 0.7998 (t70)
REVERT: A  334 GLU cc_start: 0.8320 (tt0) cc_final: 0.7949 (tm-30)
REVERT: A  354 GLU cc_start: 0.8225 (tt0) cc_final: 0.7970 (tm-30)
REVERT: A  356 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.7155 (ttp-170)
REVERT: A  357 ASP cc_start: 0.8490 (t70) cc_final: 0.8146 (t70)
REVERT: A  423 ASP cc_start: 0.8228 (m-30) cc_final: 0.7906 (t70)
REVERT: A  425 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7786 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7917 (mp0)
REVERT: A  537 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7660 (mt0)
REVERT: A  541 TYR cc_start: 0.7226 (m-10) cc_final: 0.6851 (t80)
REVERT: B   63 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8294 (tp)
REVERT: B  120 ASN cc_start: 0.8959 (t0) cc_final: 0.8518 (t0)
REVERT: B  131 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7961 (mm-30)
REVERT: B  173 PHE cc_start: 0.7400 (t80) cc_final: 0.6846 (m-80)
REVERT: B  181 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7584 (tpp80)
REVERT: B  218 ARG cc_start: 0.8304 (mtp85) cc_final: 0.8098 (mtm110)
REVERT: B  219 ARG cc_start: 0.8327 (mtp85) cc_final: 0.8009 (tpp80)
REVERT: B  255 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7683 (m-80)
REVERT: B  349 ASP cc_start: 0.8117 (t70) cc_final: 0.7770 (t0)
REVERT: B  401 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7224 (tm-30)
REVERT: B  426 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7980 (mm-30)
REVERT: B  510 GLU cc_start: 0.7144 (tt0) cc_final: 0.6367 (pp20)
REVERT: B  532 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7598 (mmm160)
REVERT: B  557 GLU cc_start: 0.8001 (mp0) cc_final: 0.7761 (mp0)
REVERT: B  574 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7282 (pttp)
REVERT: C   18 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6052 (tm)
REVERT: C   39 GLN cc_start: 0.8023 (tt0) cc_final: 0.7490 (tp40)
REVERT: C   65 LYS cc_start: 0.7949 (ptmm) cc_final: 0.7666 (pttm)
REVERT: C   82 GLN cc_start: 0.6800 (tp40) cc_final: 0.6366 (tp40)
REVERT: C   98 THR cc_start: 0.8000 (m) cc_final: 0.7625 (p)
  outliers start: 31
  outliers final: 10
  residues processed: 179
  average time/residue: 1.5824
  time to fit residues: 300.6333
Evaluate side-chains
  178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 ARG
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   79 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
C  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.138412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111951 restraints weight = 11962.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.81
r_work: 0.3109 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10398  Z= 0.214
  Angle     :  0.551   8.634  14108  Z= 0.277
  Chirality :  0.040   0.176   1606
  Planarity :  0.004   0.035   1783
  Dihedral  :  6.676  82.754   1504
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.41 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.23), residues: 1275
  helix:  1.43 (0.19), residues: 786
  sheet:  0.40 (0.48), residues: 115
  loop : -0.76 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.015   0.001   PHE A 304 
 TYR   0.015   0.001   TYR B 164 
 ARG   0.003   0.000   ARG A 255 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.7867 (mt) cc_final: 0.7497 (tt)
REVERT: A   20 ARG cc_start: 0.7843 (mtt90) cc_final: 0.7484 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8450 (mp) cc_final: 0.8185 (mm)
REVERT: A   64 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6334 (pmt-80)
REVERT: A   96 TYR cc_start: 0.8627 (t80) cc_final: 0.8426 (t80)
REVERT: A  134 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7843 (mmm)
REVERT: A  146 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7920 (mp-120)
REVERT: A  166 LEU cc_start: 0.7512 (tp) cc_final: 0.7296 (tm)
REVERT: A  218 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (tt0)
REVERT: A  232 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6968 (mp0)
REVERT: A  234 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7904 (mp0)
REVERT: A  245 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7746 (t0)
REVERT: A  255 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7856 (ttp-110)
REVERT: A  309 ASP cc_start: 0.8238 (t70) cc_final: 0.7993 (t70)
REVERT: A  334 GLU cc_start: 0.8329 (tt0) cc_final: 0.7955 (tm-30)
REVERT: A  354 GLU cc_start: 0.8228 (tt0) cc_final: 0.7971 (tm-30)
REVERT: A  356 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7160 (ttp-170)
REVERT: A  357 ASP cc_start: 0.8499 (t70) cc_final: 0.8157 (t70)
REVERT: A  377 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8302 (mmtp)
REVERT: A  423 ASP cc_start: 0.8224 (m-30) cc_final: 0.7896 (t70)
REVERT: A  425 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7778 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7959 (mp0)
REVERT: A  537 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7642 (mt0)
REVERT: A  541 TYR cc_start: 0.7223 (m-10) cc_final: 0.6889 (t80)
REVERT: B   63 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8300 (tp)
REVERT: B  120 ASN cc_start: 0.8978 (t0) cc_final: 0.8519 (t0)
REVERT: B  131 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7941 (mm-30)
REVERT: B  164 TYR cc_start: 0.8907 (m-80) cc_final: 0.8696 (m-80)
REVERT: B  173 PHE cc_start: 0.7332 (t80) cc_final: 0.6848 (m-80)
REVERT: B  181 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7660 (tpp80)
REVERT: B  218 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8103 (mtm110)
REVERT: B  219 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7962 (tpp80)
REVERT: B  255 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7678 (m-80)
REVERT: B  349 ASP cc_start: 0.8118 (t70) cc_final: 0.7770 (t0)
REVERT: B  401 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7205 (tm-30)
REVERT: B  426 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7992 (mm-30)
REVERT: B  510 GLU cc_start: 0.7156 (tt0) cc_final: 0.6365 (pp20)
REVERT: B  532 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7586 (mmm160)
REVERT: B  557 GLU cc_start: 0.8008 (mp0) cc_final: 0.7798 (mp0)
REVERT: B  570 ASP cc_start: 0.8557 (t0) cc_final: 0.8333 (t0)
REVERT: B  574 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7226 (pttp)
REVERT: C   18 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6007 (tm)
REVERT: C   39 GLN cc_start: 0.8069 (tt0) cc_final: 0.7582 (tp40)
REVERT: C   82 GLN cc_start: 0.6773 (tp40) cc_final: 0.6363 (tp-100)
REVERT: C   98 THR cc_start: 0.8011 (m) cc_final: 0.7639 (p)
  outliers start: 32
  outliers final: 8
  residues processed: 178
  average time/residue: 1.5935
  time to fit residues: 300.6230
Evaluate side-chains
  175 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 ARG
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  377 LYS
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 95 optimal weight:    0.5980
   chunk 113 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 114 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 119 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
C  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.138934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.112692 restraints weight = 11999.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.80
r_work: 0.3127 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10398  Z= 0.185
  Angle     :  0.548   8.934  14108  Z= 0.274
  Chirality :  0.040   0.187   1606
  Planarity :  0.004   0.034   1783
  Dihedral  :  6.541  82.845   1504
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.70 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.24), residues: 1275
  helix:  1.54 (0.19), residues: 786
  sheet:  0.39 (0.48), residues: 115
  loop : -0.71 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.001   TRP C  36 
 HIS   0.002   0.001   HIS B 454 
 PHE   0.028   0.001   PHE A 171 
 TYR   0.015   0.001   TYR B 164 
 ARG   0.004   0.000   ARG A 255 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.7866 (mt) cc_final: 0.7490 (tt)
REVERT: A   20 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7508 (ttp-110)
REVERT: A   33 LEU cc_start: 0.8476 (mp) cc_final: 0.8225 (mm)
REVERT: A   64 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6331 (pmt-80)
REVERT: A  134 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7869 (mmm)
REVERT: A  146 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7958 (mp-120)
REVERT: A  218 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8196 (tt0)
REVERT: A  234 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7883 (mp0)
REVERT: A  245 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7729 (t0)
REVERT: A  255 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7809 (ttp-110)
REVERT: A  309 ASP cc_start: 0.8218 (t70) cc_final: 0.7972 (t70)
REVERT: A  334 GLU cc_start: 0.8339 (tt0) cc_final: 0.7983 (tm-30)
REVERT: A  354 GLU cc_start: 0.8215 (tt0) cc_final: 0.7975 (tm-30)
REVERT: A  356 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7141 (ttp-170)
REVERT: A  357 ASP cc_start: 0.8499 (t70) cc_final: 0.8167 (t70)
REVERT: A  423 ASP cc_start: 0.8188 (m-30) cc_final: 0.7895 (t70)
REVERT: A  425 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7785 (mtm-85)
REVERT: A  431 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7983 (mp0)
REVERT: A  537 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7699 (mt0)
REVERT: A  541 TYR cc_start: 0.7232 (m-10) cc_final: 0.6897 (t80)
REVERT: B   63 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8263 (tp)
REVERT: B  120 ASN cc_start: 0.8957 (t0) cc_final: 0.8512 (t0)
REVERT: B  131 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7946 (mm-30)
REVERT: B  173 PHE cc_start: 0.7382 (t80) cc_final: 0.6859 (m-80)
REVERT: B  181 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7600 (tpp80)
REVERT: B  218 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8115 (mtm110)
REVERT: B  219 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7968 (tpp80)
REVERT: B  255 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7698 (m-80)
REVERT: B  349 ASP cc_start: 0.8091 (t70) cc_final: 0.7794 (t0)
REVERT: B  401 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7187 (tm-30)
REVERT: B  426 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7975 (mm-30)
REVERT: B  510 GLU cc_start: 0.7167 (tt0) cc_final: 0.6387 (pp20)
REVERT: B  532 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7604 (mmm160)
REVERT: B  557 GLU cc_start: 0.8018 (mp0) cc_final: 0.7811 (mp0)
REVERT: B  570 ASP cc_start: 0.8542 (t0) cc_final: 0.8332 (t0)
REVERT: B  574 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7242 (pttp)
REVERT: C   18 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6051 (tm)
REVERT: C   39 GLN cc_start: 0.8057 (tt0) cc_final: 0.7590 (tp40)
REVERT: C   65 LYS cc_start: 0.7958 (ptmm) cc_final: 0.7693 (pttt)
REVERT: C   82 GLN cc_start: 0.6763 (tp40) cc_final: 0.6356 (tp-100)
REVERT: C   98 THR cc_start: 0.8045 (m) cc_final: 0.7689 (p)
  outliers start: 28
  outliers final: 9
  residues processed: 173
  average time/residue: 1.5322
  time to fit residues: 281.5419
Evaluate side-chains
  175 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 ARG
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 GLN
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  401 GLU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   69 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 56 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
** C  77 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 = 0.3586 r_free = 0.3586 target = 0.139262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.112704 restraints weight = 11846.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.80
r_work: 0.3125 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10398  Z= 0.198
  Angle     :  0.577  11.239  14108  Z= 0.283
  Chirality :  0.040   0.198   1606
  Planarity :  0.004   0.060   1783
  Dihedral  :  6.580  82.547   1504
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.18 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.24), residues: 1275
  helix:  1.52 (0.19), residues: 786
  sheet:  0.42 (0.48), residues: 115
  loop : -0.73 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.001   TRP C  36 
 HIS   0.002   0.001   HIS B 454 
 PHE   0.020   0.001   PHE B 178 
 TYR   0.025   0.001   TYR B 164 
 ARG   0.012   0.000   ARG A 233 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7984.40 seconds
wall clock time: 141 minutes 6.61 seconds (8466.61 seconds total)