Starting phenix.real_space_refine
on Fri Mar 14 01:18:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x3e_22020/03_2025/6x3e_22020.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x3e_22020/03_2025/6x3e_22020.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x3e_22020/03_2025/6x3e_22020.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x3e_22020/03_2025/6x3e_22020.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x3e_22020/03_2025/6x3e_22020.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x3e_22020/03_2025/6x3e_22020.cif"
  }
  resolution = 3.42
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      69      5.16       5
     Na      3      4.78       5
     C    6200      2.51       5
     N    1505      2.21       5
     O    1692      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9469
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3193
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 11, 'TRANS': 407}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 411, 3132
          Classifications: {'peptide': 411}
          Link IDs: {'PTRANS': 11, 'TRANS': 399}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 411, 3132
          Classifications: {'peptide': 411}
          Link IDs: {'PTRANS': 11, 'TRANS': 399}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' NA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.22, per 1000 atoms: 0.66
  Number of scatterers: 9469
  At special positions: 0
  Unit cell: (112.32, 108.16, 86.528, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      69     16.00
     Na      3     11.00
     O    1692      8.00
     N    1505      7.00
     C    6200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2296

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 5 sheets defined
      80.8% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 42
      removed outlier: 3.767A  pdb=" N   LEU A  22 " --> pdb=" O   ASN A  18 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR A  24 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A  37 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ARG A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLU A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 53 through 81
      removed outlier: 3.541A  pdb=" N   LEU A  65 " --> pdb=" O   ARG A  61 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ILE A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LEU A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
      removed outlier: 3.845A  pdb=" N   VAL A  79 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 117
      removed outlier: 3.611A  pdb=" N   TYR A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ILE A 104 " --> pdb=" O   CYS A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.546A  pdb=" N   ASP A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ILE A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 158
    Processing helix  chain 'A' and resid 211 through 228
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 3.580A  pdb=" N   LYS A 232 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 233 through 250
      removed outlier: 3.529A  pdb=" N   VAL A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   MET A 248 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 266
      removed outlier: 4.068A  pdb=" N   CYS A 256 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TYR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      Proline residue:  A 259  - end of helix
      removed outlier: 3.554A  pdb=" N   LEU A 263 " --> pdb=" O   PRO A 259 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   PHE A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.705A  pdb=" N   PHE A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 299
      removed outlier: 4.375A  pdb=" N   THR A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY A 292 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.520A  pdb=" N   PHE A 306 " --> pdb=" O   PRO A 302 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A 308 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 320
      removed outlier: 3.682A  pdb=" N   PHE A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.540A  pdb=" N   MET A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 346
    Processing helix  chain 'A' and resid 351 through 365
      removed outlier: 3.543A  pdb=" N   ARG A 356 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   PHE A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
      removed outlier: 3.878A  pdb=" N   THR A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 384
      removed outlier: 3.983A  pdb=" N   VAL A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 408
      removed outlier: 3.823A  pdb=" N   ILE A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   THR A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.595A  pdb=" N   VAL A 422 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 436
      removed outlier: 3.556A  pdb=" N   ASP A 432 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 433 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR A 434 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A 435 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 466
      removed outlier: 3.659A  pdb=" N   PHE A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   THR A 448 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET A 449 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASN A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 471
    Processing helix  chain 'B' and resid 21 through 40
      removed outlier: 3.502A  pdb=" N   ALA B  27 " --> pdb=" O   SER B  23 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG B  39 " --> pdb=" O   GLY B  35 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU B  40 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 53
      removed outlier: 3.816A  pdb=" N   ALA B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 86
      removed outlier: 3.723A  pdb=" N   LEU B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS B  64 " --> pdb=" O   MET B  60 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   LEU B  68 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
      Proline residue:  B  69  - end of helix
      removed outlier: 3.706A  pdb=" N   SER B  84 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 117
      removed outlier: 3.641A  pdb=" N   VAL B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 150
      removed outlier: 3.584A  pdb=" N   MET B 142 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE B 146 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   PHE B 150 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 158
    Processing helix  chain 'B' and resid 211 through 230
      removed outlier: 3.551A  pdb=" N   GLY B 227 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY B 230 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 273
      Proline residue:  B 259  - end of helix
      removed outlier: 3.549A  pdb=" N   LEU B 263 " --> pdb=" O   PRO B 259 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 299
      removed outlier: 3.729A  pdb=" N   THR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 309
      removed outlier: 3.698A  pdb=" N   VAL B 308 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 319
      removed outlier: 3.524A  pdb=" N   PHE B 316 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY B 319 " --> pdb=" O   ARG B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
      removed outlier: 3.692A  pdb=" N   LEU B 325 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR B 326 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 349
      removed outlier: 4.141A  pdb=" N   ARG B 342 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ASN B 347 " --> pdb=" O   CYS B 343 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN B 349 " --> pdb=" O   GLU B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 366
      removed outlier: 4.172A  pdb=" N   PHE B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU B 359 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      Proline residue:  B 360  - end of helix
      removed outlier: 4.410A  pdb=" N   THR B 364 " --> pdb=" O   PRO B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 385
      removed outlier: 3.567A  pdb=" N   VAL B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 401
    Processing helix  chain 'B' and resid 412 through 415
      removed outlier: 3.881A  pdb=" N   GLY B 415 " --> pdb=" O   PRO B 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 412 through 415'
    Processing helix  chain 'B' and resid 416 through 427
      removed outlier: 3.780A  pdb=" N   VAL B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 432
      removed outlier: 3.572A  pdb=" N   ASP B 432 " --> pdb=" O   PRO B 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 429 through 432'
    Processing helix  chain 'B' and resid 433 through 438
    Processing helix  chain 'B' and resid 439 through 466
      removed outlier: 3.613A  pdb=" N   LEU B 443 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ARG B 445 " --> pdb=" O   TRP B 441 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   PHE B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR B 448 " --> pdb=" O   ASP B 444 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET B 449 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ASP B 455 " --> pdb=" O   ASN B 451 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR B 459 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLY B 460 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU B 463 " --> pdb=" O   THR B 459 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS B 464 " --> pdb=" O   GLY B 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 40
      removed outlier: 3.601A  pdb=" N   ALA C  27 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG C  39 " --> pdb=" O   GLY C  35 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLU C  40 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 53
      removed outlier: 3.762A  pdb=" N   ALA C  53 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 86
      removed outlier: 3.657A  pdb=" N   LEU C  59 " --> pdb=" O   PRO C  55 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS C  64 " --> pdb=" O   MET C  60 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE C  66 " --> pdb=" O   MET C  62 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   LEU C  68 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
      Proline residue:  C  69  - end of helix
      removed outlier: 3.747A  pdb=" N   SER C  84 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL C  86 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 117
      removed outlier: 3.612A  pdb=" N   VAL C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 150
      removed outlier: 3.537A  pdb=" N   MET C 142 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE C 146 " --> pdb=" O   MET C 142 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE C 150 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 158
    Processing helix  chain 'C' and resid 211 through 230
      removed outlier: 3.558A  pdb=" N   GLY C 227 " --> pdb=" O   GLY C 223 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY C 230 " --> pdb=" O   ILE C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 273
      removed outlier: 3.503A  pdb=" N   GLN C 252 " --> pdb=" O   MET C 248 " (cutoff:3.500A)
      Proline residue:  C 259  - end of helix
      removed outlier: 3.676A  pdb=" N   PHE C 264 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU C 272 " --> pdb=" O   GLY C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 299
      removed outlier: 3.716A  pdb=" N   THR C 291 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 309
      removed outlier: 3.725A  pdb=" N   VAL C 308 " --> pdb=" O   ILE C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 319
    Processing helix  chain 'C' and resid 320 through 330
      removed outlier: 3.621A  pdb=" N   THR C 326 " --> pdb=" O   GLN C 322 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET C 329 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 336 through 349
      removed outlier: 4.243A  pdb=" N   ARG C 342 " --> pdb=" O   PRO C 338 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU C 345 " --> pdb=" O   PHE C 341 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ASN C 347 " --> pdb=" O   CYS C 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 366
      removed outlier: 4.177A  pdb=" N   PHE C 357 " --> pdb=" O   ARG C 353 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU C 359 " --> pdb=" O   THR C 355 " (cutoff:3.500A)
      Proline residue:  C 360  - end of helix
      removed outlier: 4.274A  pdb=" N   THR C 364 " --> pdb=" O   PRO C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 385
      removed outlier: 3.558A  pdb=" N   VAL C 379 " --> pdb=" O   ALA C 375 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 401
      removed outlier: 3.622A  pdb=" N   THR C 396 " --> pdb=" O   GLY C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 408
    Processing helix  chain 'C' and resid 412 through 415
      removed outlier: 3.911A  pdb=" N   GLY C 415 " --> pdb=" O   PRO C 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 412 through 415'
    Processing helix  chain 'C' and resid 416 through 427
      removed outlier: 3.777A  pdb=" N   VAL C 426 " --> pdb=" O   VAL C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 432
      removed outlier: 3.591A  pdb=" N   ASP C 432 " --> pdb=" O   PRO C 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 429 through 432'
    Processing helix  chain 'C' and resid 433 through 438
    Processing helix  chain 'C' and resid 439 through 466
      removed outlier: 3.598A  pdb=" N   LEU C 443 " --> pdb=" O   VAL C 439 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ARG C 445 " --> pdb=" O   TRP C 441 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   PHE C 446 " --> pdb=" O   LEU C 442 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR C 448 " --> pdb=" O   ASP C 444 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   MET C 449 " --> pdb=" O   ARG C 445 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ASP C 455 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR C 459 " --> pdb=" O   ASP C 455 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLY C 460 " --> pdb=" O   ALA C 456 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU C 463 " --> pdb=" O   THR C 459 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LYS C 464 " --> pdb=" O   GLY C 460 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167
    Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161
    Processing sheet with id=AA3, first strand: chain 'B' and resid 164 through 167
    Processing sheet with id=AA4, first strand: chain 'C' and resid 160 through 161
    Processing sheet with id=AA5, first strand: chain 'C' and resid 164 through 167

    595 hydrogen bonds defined for protein.
    1761 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1816
        1.33 -     1.45: 1998
        1.45 -     1.57: 5666
        1.57 -     1.69: 0
        1.69 -     1.81: 123
  Bond restraints: 9603
  Sorted by residual:
  bond pdb=" N   LEU C 372 "
       pdb=" CA  LEU C 372 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.17e+00
  bond pdb=" N   LEU B  30 "
       pdb=" CA  LEU B  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.33e-02 5.65e+03 4.97e+00
  bond pdb=" N   CYS A 100 "
       pdb=" CA  CYS A 100 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.31e-02 5.83e+03 4.78e+00
  bond pdb=" N   LYS A 269 "
       pdb=" CA  LYS A 269 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.28e-02 6.10e+03 4.65e+00
  bond pdb=" N   LEU B 372 "
       pdb=" CA  LEU B 372 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.52e+00
  ... (remaining 9598 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 12305
        1.74 -     3.47: 604
        3.47 -     5.20: 71
        5.20 -     6.94: 30
        6.94 -     8.67: 17
  Bond angle restraints: 13027
  Sorted by residual:
  angle pdb=" N   GLN A 122 "
        pdb=" CA  GLN A 122 "
        pdb=" C   GLN A 122 "
      ideal   model   delta    sigma   weight residual
     110.44  102.53    7.91 1.20e+00 6.94e-01 4.35e+01
  angle pdb=" CA  LYS A 123 "
        pdb=" C   LYS A 123 "
        pdb=" N   VAL A 124 "
      ideal   model   delta    sigma   weight residual
     117.17  122.37   -5.20 1.18e+00 7.18e-01 1.94e+01
  angle pdb=" C   VAL A 120 "
        pdb=" N   THR A 121 "
        pdb=" CA  THR A 121 "
      ideal   model   delta    sigma   weight residual
     122.40  128.71   -6.31 1.45e+00 4.76e-01 1.89e+01
  angle pdb=" CA  GLN A 413 "
        pdb=" CB  GLN A 413 "
        pdb=" CG  GLN A 413 "
      ideal   model   delta    sigma   weight residual
     114.10  122.73   -8.63 2.00e+00 2.50e-01 1.86e+01
  angle pdb=" C   ASP C 388 "
        pdb=" N   LEU C 389 "
        pdb=" CA  LEU C 389 "
      ideal   model   delta    sigma   weight residual
     121.54  128.96   -7.42 1.91e+00 2.74e-01 1.51e+01
  ... (remaining 13022 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 5202
       17.90 -    35.79: 437
       35.79 -    53.68: 84
       53.68 -    71.58: 17
       71.58 -    89.47: 10
  Dihedral angle restraints: 5750
    sinusoidal: 2192
      harmonic: 3558
  Sorted by residual:
  dihedral pdb=" CA  GLU A 272 "
           pdb=" C   GLU A 272 "
           pdb=" N   VAL A 273 "
           pdb=" CA  VAL A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.11  -21.89     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  LEU B 384 "
           pdb=" C   LEU B 384 "
           pdb=" N   ASN B 385 "
           pdb=" CA  ASN B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.31   19.69     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  LEU C 384 "
           pdb=" C   LEU C 384 "
           pdb=" N   ASN C 385 "
           pdb=" CA  ASN C 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 5747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1388
       0.070 -    0.141: 237
       0.141 -    0.211: 21
       0.211 -    0.281: 7
       0.281 -    0.352: 1
  Chirality restraints: 1654
  Sorted by residual:
  chirality pdb=" CB  VAL A 411 "
            pdb=" CA  VAL A 411 "
            pdb=" CG1 VAL A 411 "
            pdb=" CG2 VAL A 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CB  ILE A 278 "
            pdb=" CA  ILE A 278 "
            pdb=" CG1 ILE A 278 "
            pdb=" CG2 ILE A 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CB  VAL A 426 "
            pdb=" CA  VAL A 426 "
            pdb=" CG1 VAL A 426 "
            pdb=" CG2 VAL A 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 1651 not shown)

  Planarity restraints: 1585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 301 "   -0.047 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO B 302 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B 302 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 302 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 301 "   -0.046 5.00e-02 4.00e+02   6.93e-02 7.68e+00
        pdb=" N   PRO C 302 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO C 302 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 302 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 301 "   -0.042 5.00e-02 4.00e+02   6.21e-02 6.17e+00
        pdb=" N   PRO A 302 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 302 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 302 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1582 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 82
        2.65 -     3.21: 8339
        3.21 -     3.77: 14585
        3.77 -     4.34: 20502
        4.34 -     4.90: 33380
  Nonbonded interactions: 76888
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 368 "
            pdb="NA    NA A 603 "
     model   vdw
     2.083 2.470
  nonbonded pdb=" OD1 ASN A 366 "
            pdb="NA    NA A 603 "
     model   vdw
     2.228 2.470
  nonbonded pdb=" O   ASN A 366 "
            pdb="NA    NA A 601 "
     model   vdw
     2.293 2.470
  nonbonded pdb=" O   PRO B  69 "
            pdb=" OG  SER B  73 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ALA A 456 "
            pdb=" OG1 THR A 459 "
     model   vdw
     2.317 3.040
  ... (remaining 76883 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 19 through 121 or resid 137 through 474))
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.450
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.400
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   9603  Z= 0.346
  Angle     :  0.904   8.675  13027  Z= 0.500
  Chirality :  0.055   0.352   1654
  Planarity :  0.007   0.070   1585
  Dihedral  : 14.423  89.473   3454
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.31 %
    Favored  : 88.69 %
  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: -6.06 (0.15), residues: 1223
  helix: -4.16 (0.08), residues: 954
  sheet: -2.40 (0.81), residues: 54
  loop : -1.89 (0.34), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 276 
 HIS   0.003   0.001   HIS C  41 
 PHE   0.022   0.003   PHE B 159 
 TYR   0.024   0.002   TYR C 373 
 ARG   0.003   0.001   ARG B  39 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.9037 (mp) cc_final: 0.8808 (tp)
REVERT: A  112 LEU cc_start: 0.8818 (mt) cc_final: 0.8537 (mt)
REVERT: A  277 GLU cc_start: 0.8270 (tp30) cc_final: 0.7885 (tp30)
REVERT: B   19 TRP cc_start: 0.7039 (t60) cc_final: 0.5389 (m100)
REVERT: B   93 ARG cc_start: 0.8504 (mtt180) cc_final: 0.7722 (mtt180)
REVERT: B  140 ASP cc_start: 0.7915 (m-30) cc_final: 0.7557 (m-30)
REVERT: B  228 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7889 (mmmt)
REVERT: B  280 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7459 (tpt170)
REVERT: B  354 ILE cc_start: 0.8661 (mt) cc_final: 0.8310 (mm)
REVERT: B  444 ASP cc_start: 0.8898 (t0) cc_final: 0.8466 (t0)
REVERT: B  465 LEU cc_start: 0.8761 (mt) cc_final: 0.8457 (mt)
REVERT: C   97 TYR cc_start: 0.9153 (t80) cc_final: 0.8689 (t80)
REVERT: C  397 ILE cc_start: 0.9506 (mm) cc_final: 0.9256 (mm)
REVERT: C  446 PHE cc_start: 0.8519 (m-80) cc_final: 0.8242 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.2170
  time to fit residues: 88.9324
Evaluate side-chains
  198 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 93 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 62 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 153 ASN
B 348 ASN
C 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.130260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.095593 restraints weight = 15284.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 2.03
r_work: 0.2959 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9603  Z= 0.156
  Angle     :  0.601   8.191  13027  Z= 0.305
  Chirality :  0.040   0.148   1654
  Planarity :  0.005   0.037   1585
  Dihedral  :  4.580  18.303   1302
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.20 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.20), residues: 1223
  helix: -1.78 (0.14), residues: 953
  sheet: -2.19 (0.77), residues: 54
  loop : -2.05 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 441 
 HIS   0.000   0.000   HIS A 296 
 PHE   0.019   0.002   PHE C 306 
 TYR   0.010   0.001   TYR B 305 
 ARG   0.006   0.001   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 224
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.9056 (mp) cc_final: 0.8750 (tp)
REVERT: A   40 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7340 (mp0)
REVERT: A  112 LEU cc_start: 0.8353 (mt) cc_final: 0.8104 (mt)
REVERT: A  205 MET cc_start: 0.8566 (pmm) cc_final: 0.8333 (ptm)
REVERT: A  277 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7267 (tp30)
REVERT: A  463 GLU cc_start: 0.8569 (tt0) cc_final: 0.7876 (tm-30)
REVERT: A  473 MET cc_start: 0.4466 (mtt) cc_final: 0.4161 (ptp)
REVERT: B   19 TRP cc_start: 0.7198 (t60) cc_final: 0.5420 (m100)
REVERT: B  220 LEU cc_start: 0.9230 (tt) cc_final: 0.8352 (mt)
REVERT: B  320 MET cc_start: 0.8355 (mmm) cc_final: 0.8044 (mpp)
REVERT: B  354 ILE cc_start: 0.8642 (mt) cc_final: 0.8348 (mm)
REVERT: B  368 ASP cc_start: 0.9264 (m-30) cc_final: 0.8956 (m-30)
REVERT: B  449 MET cc_start: 0.8445 (tmm) cc_final: 0.8169 (tmm)
REVERT: C   97 TYR cc_start: 0.8971 (t80) cc_final: 0.8635 (t80)
REVERT: C  206 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7502 (t80)
REVERT: C  446 PHE cc_start: 0.8871 (m-80) cc_final: 0.8655 (m-80)
  outliers start: 23
  outliers final: 13
  residues processed: 235
  average time/residue: 0.1849
  time to fit residues: 63.7779
Evaluate side-chains
  193 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  304 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  373 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 109 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    4.9990
   chunk 51 optimal weight:    0.3980
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 53 optimal weight:    0.2980
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 110 optimal weight:    0.0970
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.131371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.096764 restraints weight = 15169.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.04
r_work: 0.2975 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9603  Z= 0.128
  Angle     :  0.543   8.287  13027  Z= 0.271
  Chirality :  0.038   0.162   1654
  Planarity :  0.004   0.028   1585
  Dihedral  :  4.153  17.660   1302
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.18 %
    Favored  : 78.33 %
  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: -1.24 (0.23), residues: 1223
  helix: -0.34 (0.17), residues: 947
  sheet: -1.86 (0.77), residues: 54
  loop : -2.04 (0.38), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 441 
 HIS   0.001   0.000   HIS A 296 
 PHE   0.020   0.001   PHE B 357 
 TYR   0.014   0.001   TYR A 305 
 ARG   0.006   0.000   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 204
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.9026 (mp) cc_final: 0.8689 (tp)
REVERT: A  277 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8260 (tp30)
REVERT: A  455 ASP cc_start: 0.8098 (m-30) cc_final: 0.7795 (m-30)
REVERT: A  473 MET cc_start: 0.4389 (mtt) cc_final: 0.4078 (ptp)
REVERT: B   19 TRP cc_start: 0.7295 (t60) cc_final: 0.5405 (m100)
REVERT: B  220 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8343 (mt)
REVERT: B  354 ILE cc_start: 0.8593 (mt) cc_final: 0.8365 (mm)
REVERT: B  367 MET cc_start: 0.8437 (mmm) cc_final: 0.8102 (mmp)
REVERT: B  413 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7307 (mm110)
REVERT: B  449 MET cc_start: 0.8377 (tmm) cc_final: 0.8073 (tmm)
REVERT: C   97 TYR cc_start: 0.8935 (t80) cc_final: 0.8595 (t80)
REVERT: C  206 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7607 (t80)
  outliers start: 26
  outliers final: 10
  residues processed: 216
  average time/residue: 0.2885
  time to fit residues: 91.6487
Evaluate side-chains
  185 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 2.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  206 TYR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  373 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 HIS
B 296 HIS
B 472 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.127364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.091711 restraints weight = 15215.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.03
r_work: 0.2897 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9603  Z= 0.236
  Angle     :  0.579  10.592  13027  Z= 0.291
  Chirality :  0.040   0.142   1654
  Planarity :  0.004   0.028   1585
  Dihedral  :  4.145  18.896   1302
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.56 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1223
  helix:  0.11 (0.17), residues: 959
  sheet: -1.64 (0.76), residues: 54
  loop : -1.74 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 441 
 HIS   0.002   0.001   HIS A 296 
 PHE   0.021   0.002   PHE A 306 
 TYR   0.018   0.001   TYR A 285 
 ARG   0.006   0.001   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  277 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8288 (tp30)
REVERT: A  463 GLU cc_start: 0.8582 (tt0) cc_final: 0.8171 (tm-30)
REVERT: A  473 MET cc_start: 0.4566 (mtt) cc_final: 0.4179 (ptp)
REVERT: B   19 TRP cc_start: 0.7307 (t60) cc_final: 0.5446 (m100)
REVERT: B  220 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8342 (mt)
REVERT: B  280 ARG cc_start: 0.8569 (ttp80) cc_final: 0.7579 (tpt170)
REVERT: B  449 MET cc_start: 0.8449 (tmm) cc_final: 0.8126 (tmm)
REVERT: B  472 GLN cc_start: 0.7327 (mt0) cc_final: 0.7066 (mm110)
REVERT: C  206 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7342 (t80)
REVERT: C  320 MET cc_start: 0.7844 (mmm) cc_final: 0.7562 (mmm)
REVERT: C  399 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9231 (mp)
  outliers start: 31
  outliers final: 18
  residues processed: 190
  average time/residue: 0.2005
  time to fit residues: 55.6207
Evaluate side-chains
  182 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  276 TRP
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  364 THR
Chi-restraints excluded: chain C residue  367 MET
Chi-restraints excluded: chain C residue  373 TYR
Chi-restraints excluded: chain C residue  399 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0370
   chunk 120 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.1664

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 393 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.128980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.093951 restraints weight = 15198.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.97
r_work: 0.2942 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9603  Z= 0.164
  Angle     :  0.545  10.166  13027  Z= 0.270
  Chirality :  0.039   0.162   1654
  Planarity :  0.003   0.032   1585
  Dihedral  :  3.997  18.602   1302
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.04 %
    Favored  : 77.09 %
  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: -0.04 (0.25), residues: 1223
  helix:  0.53 (0.18), residues: 961
  sheet: -1.55 (0.75), residues: 54
  loop : -1.82 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 441 
 HIS   0.001   0.000   HIS A 296 
 PHE   0.023   0.002   PHE B 357 
 TYR   0.017   0.001   TYR C  98 
 ARG   0.006   0.000   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 1.679 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7976 (tp30)
REVERT: A  419 MET cc_start: 0.8442 (tpt) cc_final: 0.8160 (tpt)
REVERT: A  473 MET cc_start: 0.4622 (mtt) cc_final: 0.4200 (ptp)
REVERT: B   19 TRP cc_start: 0.7424 (t60) cc_final: 0.5432 (m100)
REVERT: B  164 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8801 (p)
REVERT: B  220 LEU cc_start: 0.9255 (tt) cc_final: 0.8261 (mt)
REVERT: B  280 ARG cc_start: 0.8525 (ttp80) cc_final: 0.7710 (tpt170)
REVERT: B  329 MET cc_start: 0.7969 (mmp) cc_final: 0.7595 (tpp)
REVERT: B  449 MET cc_start: 0.8327 (tmm) cc_final: 0.7996 (tmm)
REVERT: B  467 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7571 (pttm)
REVERT: B  472 GLN cc_start: 0.7309 (mt0) cc_final: 0.7041 (mm110)
REVERT: C  206 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7439 (t80)
REVERT: C  320 MET cc_start: 0.7824 (mmm) cc_final: 0.7539 (mmm)
REVERT: C  399 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9172 (mp)
  outliers start: 30
  outliers final: 22
  residues processed: 186
  average time/residue: 0.2464
  time to fit residues: 67.9803
Evaluate side-chains
  184 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  276 TRP
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  304 ILE
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  332 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  364 THR
Chi-restraints excluded: chain C residue  367 MET
Chi-restraints excluded: chain C residue  373 TYR
Chi-restraints excluded: chain C residue  399 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 115 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.127205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.094088 restraints weight = 15249.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.96
r_work: 0.2910 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9603  Z= 0.217
  Angle     :  0.561   8.173  13027  Z= 0.279
  Chirality :  0.040   0.188   1654
  Planarity :  0.003   0.031   1585
  Dihedral  :  4.016  18.514   1302
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.61 %
    Favored  : 75.93 %
  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:  0.18 (0.25), residues: 1223
  helix:  0.67 (0.18), residues: 963
  sheet: -1.56 (0.75), residues: 54
  loop : -1.66 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 441 
 HIS   0.008   0.001   HIS A 296 
 PHE   0.019   0.002   PHE B  99 
 TYR   0.018   0.001   TYR C  98 
 ARG   0.007   0.000   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8082 (tp30)
REVERT: A  280 ARG cc_start: 0.6080 (mtt180) cc_final: 0.4887 (tpt-90)
REVERT: A  463 GLU cc_start: 0.8611 (tt0) cc_final: 0.8239 (tm-30)
REVERT: B   19 TRP cc_start: 0.7380 (t60) cc_final: 0.5393 (m100)
REVERT: B  220 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8249 (mt)
REVERT: B  280 ARG cc_start: 0.8586 (ttp80) cc_final: 0.7751 (tpt170)
REVERT: B  329 MET cc_start: 0.8034 (mmp) cc_final: 0.7689 (tpp)
REVERT: B  449 MET cc_start: 0.8351 (tmm) cc_final: 0.8012 (tmm)
REVERT: B  472 GLN cc_start: 0.7369 (mt0) cc_final: 0.7121 (mm110)
REVERT: C   23 SER cc_start: 0.9061 (t) cc_final: 0.8812 (p)
REVERT: C   60 MET cc_start: 0.9238 (mmm) cc_final: 0.8973 (mmp)
REVERT: C  312 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7819 (t0)
REVERT: C  320 MET cc_start: 0.7793 (mmm) cc_final: 0.7501 (mmm)
REVERT: C  399 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9201 (mp)
  outliers start: 36
  outliers final: 24
  residues processed: 188
  average time/residue: 0.1801
  time to fit residues: 49.5407
Evaluate side-chains
  188 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  276 TRP
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  304 ILE
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  312 ASN
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  332 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  364 THR
Chi-restraints excluded: chain C residue  367 MET
Chi-restraints excluded: chain C residue  373 TYR
Chi-restraints excluded: chain C residue  399 ILE
Chi-restraints excluded: chain C residue  448 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 10 optimal weight:   30.0000
   chunk 2 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.128324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.093353 restraints weight = 15285.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.94
r_work: 0.2936 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9603  Z= 0.171
  Angle     :  0.536   7.458  13027  Z= 0.266
  Chirality :  0.040   0.227   1654
  Planarity :  0.003   0.033   1585
  Dihedral  :  3.926  17.692   1302
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.09 %
    Favored  : 75.93 %
  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:  0.47 (0.25), residues: 1223
  helix:  0.91 (0.18), residues: 959
  sheet: -1.54 (0.75), residues: 54
  loop : -1.67 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 441 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.025   0.001   PHE B 357 
 TYR   0.025   0.001   TYR C  98 
 ARG   0.006   0.000   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 170
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8024 (tp30)
REVERT: A  280 ARG cc_start: 0.6160 (mtt180) cc_final: 0.4958 (tpt-90)
REVERT: A  463 GLU cc_start: 0.8530 (tt0) cc_final: 0.8180 (tm-30)
REVERT: B   19 TRP cc_start: 0.7401 (t60) cc_final: 0.5394 (m100)
REVERT: B  164 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8734 (p)
REVERT: B  220 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8180 (mt)
REVERT: B  280 ARG cc_start: 0.8550 (ttp80) cc_final: 0.7725 (tpt170)
REVERT: B  329 MET cc_start: 0.8000 (mmp) cc_final: 0.7655 (tpp)
REVERT: B  449 MET cc_start: 0.8360 (tmm) cc_final: 0.8013 (tmm)
REVERT: C   23 SER cc_start: 0.9035 (t) cc_final: 0.8834 (p)
REVERT: C  206 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7285 (t80)
REVERT: C  312 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7815 (t0)
REVERT: C  399 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9163 (mp)
  outliers start: 31
  outliers final: 23
  residues processed: 191
  average time/residue: 0.1847
  time to fit residues: 51.5499
Evaluate side-chains
  186 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  276 TRP
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  312 ASN
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  332 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  364 THR
Chi-restraints excluded: chain C residue  367 MET
Chi-restraints excluded: chain C residue  373 TYR
Chi-restraints excluded: chain C residue  399 ILE
Chi-restraints excluded: chain C residue  433 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.126931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.091908 restraints weight = 15370.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.96
r_work: 0.2907 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9603  Z= 0.224
  Angle     :  0.575   8.367  13027  Z= 0.283
  Chirality :  0.041   0.204   1654
  Planarity :  0.003   0.033   1585
  Dihedral  :  4.003  17.284   1302
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.28 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1223
  helix:  0.92 (0.18), residues: 959
  sheet: -1.56 (0.75), residues: 54
  loop : -1.63 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP B 441 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.020   0.002   PHE B  99 
 TYR   0.025   0.001   TYR C  98 
 ARG   0.007   0.000   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8053 (tp30)
REVERT: A  280 ARG cc_start: 0.6202 (mtt180) cc_final: 0.4988 (tpt-90)
REVERT: A  463 GLU cc_start: 0.8594 (tt0) cc_final: 0.8199 (tm-30)
REVERT: B   19 TRP cc_start: 0.7466 (t60) cc_final: 0.5403 (m100)
REVERT: B  220 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8186 (mt)
REVERT: B  280 ARG cc_start: 0.8568 (ttp80) cc_final: 0.7735 (tpt170)
REVERT: B  449 MET cc_start: 0.8363 (tmm) cc_final: 0.8017 (tmm)
REVERT: C  312 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7847 (t0)
REVERT: C  399 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9171 (mp)
  outliers start: 37
  outliers final: 28
  residues processed: 191
  average time/residue: 0.1734
  time to fit residues: 48.9392
Evaluate side-chains
  187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  276 TRP
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  290 LEU
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  312 ASN
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  332 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  364 THR
Chi-restraints excluded: chain C residue  373 TYR
Chi-restraints excluded: chain C residue  399 ILE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  448 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 10 optimal weight:   30.0000
   chunk 72 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   chunk 108 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.129530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.094945 restraints weight = 15184.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.96
r_work: 0.2955 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9603  Z= 0.140
  Angle     :  0.545   7.889  13027  Z= 0.266
  Chirality :  0.039   0.206   1654
  Planarity :  0.003   0.035   1585
  Dihedral  :  3.877  16.357   1302
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.15 %
    Favored  : 74.98 %
  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:  0.76 (0.25), residues: 1223
  helix:  1.14 (0.18), residues: 958
  sheet: -1.51 (0.74), residues: 54
  loop : -1.69 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP B 441 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.029   0.001   PHE B 357 
 TYR   0.026   0.001   TYR C  98 
 ARG   0.006   0.000   ARG B 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 TYR cc_start: 0.8411 (t80) cc_final: 0.8170 (t80)
REVERT: A  277 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8036 (tp30)
REVERT: A  280 ARG cc_start: 0.6250 (mtt180) cc_final: 0.5028 (tpt-90)
REVERT: B   19 TRP cc_start: 0.7402 (t60) cc_final: 0.5356 (m100)
REVERT: B  164 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8745 (p)
REVERT: B  220 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8152 (mt)
REVERT: B  280 ARG cc_start: 0.8490 (ttp80) cc_final: 0.7761 (tpt170)
REVERT: B  447 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.8198 (mtm-85)
REVERT: B  449 MET cc_start: 0.8374 (tmm) cc_final: 0.8039 (tmm)
REVERT: C  206 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7348 (t80)
REVERT: C  312 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7805 (t0)
REVERT: C  399 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9158 (mp)
  outliers start: 30
  outliers final: 17
  residues processed: 185
  average time/residue: 0.2538
  time to fit residues: 69.2520
Evaluate side-chains
  181 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  276 TRP
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  312 ASN
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  332 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  364 THR
Chi-restraints excluded: chain C residue  373 TYR
Chi-restraints excluded: chain C residue  399 ILE
Chi-restraints excluded: chain C residue  433 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 112 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0770
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
A 296 HIS
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.130355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.095849 restraints weight = 15256.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.96
r_work: 0.2973 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9603  Z= 0.139
  Angle     :  0.562   9.968  13027  Z= 0.269
  Chirality :  0.039   0.188   1654
  Planarity :  0.003   0.036   1585
  Dihedral  :  3.822  15.651   1302
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.53 %
    Favored  : 75.07 %
  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:  0.94 (0.25), residues: 1223
  helix:  1.31 (0.18), residues: 951
  sheet: -1.37 (0.74), residues: 54
  loop : -1.77 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 441 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.022   0.001   PHE B  99 
 TYR   0.026   0.001   TYR C  98 
 ARG   0.007   0.000   ARG A 342 

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 TYR cc_start: 0.8367 (t80) cc_final: 0.8160 (t80)
REVERT: A  277 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7834 (tp30)
REVERT: A  280 ARG cc_start: 0.6116 (mtt180) cc_final: 0.4882 (tpt-90)
REVERT: B   19 TRP cc_start: 0.7405 (t60) cc_final: 0.5341 (m100)
REVERT: B  164 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8718 (p)
REVERT: B  220 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8151 (mt)
REVERT: B  280 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7755 (tpt170)
REVERT: B  447 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8263 (mtm-85)
REVERT: B  449 MET cc_start: 0.8379 (tmm) cc_final: 0.8038 (tmm)
REVERT: C  206 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7345 (t80)
REVERT: C  312 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7816 (t0)
REVERT: C  399 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9142 (mp)
  outliers start: 25
  outliers final: 15
  residues processed: 186
  average time/residue: 0.1979
  time to fit residues: 53.6795
Evaluate side-chains
  179 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain C residue  206 TYR
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  312 ASN
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  332 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  373 TYR
Chi-restraints excluded: chain C residue  399 ILE
Chi-restraints excluded: chain C residue  433 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 95 optimal weight:    0.5980
   chunk 117 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.129317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.094600 restraints weight = 15172.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.94
r_work: 0.2955 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.4174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9603  Z= 0.167
  Angle     :  0.574   9.446  13027  Z= 0.277
  Chirality :  0.040   0.184   1654
  Planarity :  0.003   0.034   1585
  Dihedral  :  3.846  15.757   1302
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 23.11 %
    Favored  : 74.78 %
  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:  0.96 (0.25), residues: 1223
  helix:  1.32 (0.18), residues: 949
  sheet: -1.34 (0.73), residues: 54
  loop : -1.72 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 441 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.028   0.001   PHE B 357 
 TYR   0.026   0.001   TYR C  98 
 ARG   0.007   0.000   ARG A 342 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5217.55 seconds
wall clock time: 93 minutes 21.48 seconds (5601.48 seconds total)