Starting phenix.real_space_refine
on Fri Mar 14 05:48:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6gct_4386/03_2025/6gct_4386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6gct_4386/03_2025/6gct_4386.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6gct_4386/03_2025/6gct_4386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6gct_4386/03_2025/6gct_4386.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6gct_4386/03_2025/6gct_4386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6gct_4386/03_2025/6gct_4386.cif"
  }
  resolution = 3.85
  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=   0.007
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: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6324      2.51       5
     N    1605      2.21       5
     O    1695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9672
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3214
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 16, 'TRANS': 415}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 6.23, per 1000 atoms: 0.64
  Number of scatterers: 9672
  At special positions: 0
  Unit cell: (117.392, 119.416, 82.984, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1695      8.00
     N    1605      7.00
     C    6324      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: 2.48
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 6 sheets defined
      75.5% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 52
      removed outlier: 3.789A  pdb=" N   ARG A  50 " --> pdb=" O   ARG A  46 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A  51 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN A  52 " --> pdb=" O   CYS A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 46 through 52'
    Processing helix  chain 'A' and resid 52 through 76
      removed outlier: 3.913A  pdb=" N   VAL A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A  62 " --> pdb=" O   THR A  58 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA A  67 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 90 through 118
      removed outlier: 3.910A  pdb=" N   LEU A  96 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 3.674A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU A 112 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLY A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLY A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER A 118 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 154
      removed outlier: 3.618A  pdb=" N   LEU A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   VAL A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ALA A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 192
      removed outlier: 3.652A  pdb=" N   PHE A 192 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 200
    Processing helix  chain 'A' and resid 234 through 249
      removed outlier: 3.878A  pdb=" N   ALA A 244 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 252
      No H-bonds generated for 'chain 'A' and resid 250 through 252'
    Processing helix  chain 'A' and resid 253 through 263
      removed outlier: 3.823A  pdb=" N   SER A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 290
      removed outlier: 4.113A  pdb=" N   TRP A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR A 276 " --> pdb=" O   TRP A 272 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
      removed outlier: 3.705A  pdb=" N   MET A 282 " --> pdb=" O   PRO A 278 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   PHE A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 286 " --> pdb=" O   MET A 282 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 287 " --> pdb=" O   PHE A 283 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A 288 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 319
      removed outlier: 3.693A  pdb=" N   TYR A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 330
      removed outlier: 3.695A  pdb=" N   PHE A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 338
      removed outlier: 3.558A  pdb=" N   TRP A 338 " --> pdb=" O   TYR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 351
      removed outlier: 3.529A  pdb=" N   LEU A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   PHE A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
      removed outlier: 4.158A  pdb=" N   MET A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU A 365 " --> pdb=" O   MET A 361 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   GLU A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 376
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 387 through 398
      removed outlier: 3.551A  pdb=" N   CYS A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'A' and resid 410 through 424
      removed outlier: 3.553A  pdb=" N   THR A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ALA A 421 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 441
      removed outlier: 3.641A  pdb=" N   THR A 438 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 446
    Processing helix  chain 'A' and resid 449 through 452
      removed outlier: 3.560A  pdb=" N   HIS A 452 " --> pdb=" O   PRO A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 449 through 452'
    Processing helix  chain 'A' and resid 453 through 458
    Processing helix  chain 'A' and resid 459 through 487
      removed outlier: 3.558A  pdb=" N   VAL A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ARG A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LEU A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASP A 475 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A 476 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN A 484 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 52
      removed outlier: 3.789A  pdb=" N   ARG B  50 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B  51 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN B  52 " --> pdb=" O   CYS B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 46 through 52'
    Processing helix  chain 'B' and resid 52 through 76
      removed outlier: 3.912A  pdb=" N   VAL B  59 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL B  62 " --> pdb=" O   THR B  58 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 89
    Processing helix  chain 'B' and resid 90 through 118
      removed outlier: 3.909A  pdb=" N   LEU B  96 " --> pdb=" O   PRO B  92 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   LEU B  99 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
      removed outlier: 3.674A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU B 112 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE B 113 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLY B 114 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLY B 115 " --> pdb=" O   SER B 111 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   SER B 118 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 154
      removed outlier: 3.617A  pdb=" N   LEU B 132 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU B 145 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA B 152 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 192
      removed outlier: 3.651A  pdb=" N   PHE B 192 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 200
    Processing helix  chain 'B' and resid 234 through 249
      removed outlier: 3.878A  pdb=" N   ALA B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 252
      No H-bonds generated for 'chain 'B' and resid 250 through 252'
    Processing helix  chain 'B' and resid 253 through 263
      removed outlier: 3.823A  pdb=" N   SER B 261 " --> pdb=" O   ARG B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 290
      removed outlier: 4.114A  pdb=" N   TRP B 272 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR B 276 " --> pdb=" O   TRP B 272 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
      removed outlier: 3.705A  pdb=" N   MET B 282 " --> pdb=" O   PRO B 278 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   PHE B 283 " --> pdb=" O   VAL B 279 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU B 284 " --> pdb=" O   GLY B 280 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA B 286 " --> pdb=" O   MET B 282 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY B 287 " --> pdb=" O   PHE B 283 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 319
      removed outlier: 3.692A  pdb=" N   TYR B 305 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 319 " --> pdb=" O   ILE B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 330
      removed outlier: 3.695A  pdb=" N   PHE B 328 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 338
      removed outlier: 3.558A  pdb=" N   TRP B 338 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
      removed outlier: 3.530A  pdb=" N   LEU B 344 " --> pdb=" O   ILE B 340 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE B 348 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 368
      removed outlier: 4.157A  pdb=" N   MET B 361 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLU B 365 " --> pdb=" O   MET B 361 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   GLU B 366 " --> pdb=" O   LYS B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 376
    Processing helix  chain 'B' and resid 378 through 383
    Processing helix  chain 'B' and resid 387 through 398
      removed outlier: 3.551A  pdb=" N   CYS B 395 " --> pdb=" O   ALA B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 405
    Processing helix  chain 'B' and resid 410 through 424
      removed outlier: 3.552A  pdb=" N   THR B 416 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 418 " --> pdb=" O   ILE B 414 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR B 420 " --> pdb=" O   THR B 416 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ALA B 421 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 441
      removed outlier: 3.642A  pdb=" N   THR B 438 " --> pdb=" O   GLY B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 446
    Processing helix  chain 'B' and resid 449 through 452
      removed outlier: 3.562A  pdb=" N   HIS B 452 " --> pdb=" O   PRO B 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 449 through 452'
    Processing helix  chain 'B' and resid 453 through 458
    Processing helix  chain 'B' and resid 459 through 487
      removed outlier: 3.558A  pdb=" N   VAL B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ARG B 465 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   LEU B 470 " --> pdb=" O   SER B 466 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA B 476 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN B 484 " --> pdb=" O   GLY B 480 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 52
      removed outlier: 3.790A  pdb=" N   ARG C  50 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA C  51 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASN C  52 " --> pdb=" O   CYS C  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 46 through 52'
    Processing helix  chain 'C' and resid 52 through 76
      removed outlier: 3.912A  pdb=" N   VAL C  59 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL C  62 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA C  67 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 89
    Processing helix  chain 'C' and resid 90 through 118
      removed outlier: 3.910A  pdb=" N   LEU C  96 " --> pdb=" O   PRO C  92 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU C  97 " --> pdb=" O   GLY C  93 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LEU C  99 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG C 101 " --> pdb=" O   LEU C  97 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE C 103 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE C 104 " --> pdb=" O   LEU C 100 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU C 105 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      Proline residue:  C 106  - end of helix
      removed outlier: 3.675A  pdb=" N   VAL C 109 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   LEU C 112 " --> pdb=" O   VAL C 108 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLY C 114 " --> pdb=" O   CYS C 110 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLY C 115 " --> pdb=" O   SER C 111 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER C 118 " --> pdb=" O   GLY C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 154
      removed outlier: 3.617A  pdb=" N   LEU C 132 " --> pdb=" O   GLY C 128 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU C 145 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   VAL C 147 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ALA C 152 " --> pdb=" O   GLY C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 192
      removed outlier: 3.651A  pdb=" N   PHE C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 200
    Processing helix  chain 'C' and resid 234 through 249
      removed outlier: 3.878A  pdb=" N   ALA C 244 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG C 246 " --> pdb=" O   GLY C 242 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY C 249 " --> pdb=" O   LEU C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 252
      No H-bonds generated for 'chain 'C' and resid 250 through 252'
    Processing helix  chain 'C' and resid 253 through 263
      removed outlier: 3.824A  pdb=" N   SER C 261 " --> pdb=" O   ARG C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 290
      removed outlier: 4.114A  pdb=" N   TRP C 272 " --> pdb=" O   VAL C 268 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR C 276 " --> pdb=" O   TRP C 272 " (cutoff:3.500A)
      Proline residue:  C 278  - end of helix
      removed outlier: 3.706A  pdb=" N   MET C 282 " --> pdb=" O   PRO C 278 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   PHE C 283 " --> pdb=" O   VAL C 279 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU C 284 " --> pdb=" O   GLY C 280 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA C 286 " --> pdb=" O   MET C 282 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY C 287 " --> pdb=" O   PHE C 283 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS C 288 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL C 290 " --> pdb=" O   ALA C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 319
      removed outlier: 3.693A  pdb=" N   TYR C 305 " --> pdb=" O   ARG C 301 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU C 307 " --> pdb=" O   GLY C 303 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU C 319 " --> pdb=" O   ILE C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 330
      removed outlier: 3.695A  pdb=" N   PHE C 328 " --> pdb=" O   ILE C 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 338
      removed outlier: 3.558A  pdb=" N   TRP C 338 " --> pdb=" O   TYR C 334 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 351
      removed outlier: 3.530A  pdb=" N   LEU C 344 " --> pdb=" O   ILE C 340 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE C 348 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 368
      removed outlier: 4.158A  pdb=" N   MET C 361 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLU C 365 " --> pdb=" O   MET C 361 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   GLU C 366 " --> pdb=" O   LYS C 362 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 376
    Processing helix  chain 'C' and resid 378 through 383
    Processing helix  chain 'C' and resid 387 through 398
      removed outlier: 3.551A  pdb=" N   CYS C 395 " --> pdb=" O   ALA C 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 405
    Processing helix  chain 'C' and resid 410 through 424
      removed outlier: 3.552A  pdb=" N   THR C 416 " --> pdb=" O   VAL C 412 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU C 418 " --> pdb=" O   ILE C 414 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR C 420 " --> pdb=" O   THR C 416 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ALA C 421 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 434 through 441
      removed outlier: 3.641A  pdb=" N   THR C 438 " --> pdb=" O   GLY C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 441 through 446
    Processing helix  chain 'C' and resid 449 through 452
      removed outlier: 3.562A  pdb=" N   HIS C 452 " --> pdb=" O   PRO C 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 449 through 452'
    Processing helix  chain 'C' and resid 453 through 458
    Processing helix  chain 'C' and resid 459 through 487
      removed outlier: 3.557A  pdb=" N   VAL C 463 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   ARG C 465 " --> pdb=" O   TRP C 461 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL C 469 " --> pdb=" O   ARG C 465 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LEU C 470 " --> pdb=" O   SER C 466 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA C 476 " --> pdb=" O   VAL C 472 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN C 484 " --> pdb=" O   GLY C 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 203
    Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209
    Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 203
    Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 209
    Processing sheet with id=AA5, first strand: chain 'C' and resid 202 through 203
    Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 209

    501 hydrogen bonds defined for protein.
    1440 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: 2.70

  Time building geometry restraints manager: 2.95 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: 2698
        1.33 -     1.45: 1748
        1.45 -     1.57: 5319
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 9840
  Sorted by residual:
  bond pdb=" CA  MET C 387 "
       pdb=" CB  MET C 387 "
    ideal  model  delta    sigma   weight residual
    1.539  1.399  0.140 4.88e-02 4.20e+02 8.26e+00
  bond pdb=" CA  MET B 387 "
       pdb=" CB  MET B 387 "
    ideal  model  delta    sigma   weight residual
    1.539  1.399  0.140 4.88e-02 4.20e+02 8.25e+00
  bond pdb=" CA  MET A 387 "
       pdb=" CB  MET A 387 "
    ideal  model  delta    sigma   weight residual
    1.539  1.400  0.140 4.88e-02 4.20e+02 8.20e+00
  bond pdb=" CB  ASN C 190 "
       pdb=" CG  ASN C 190 "
    ideal  model  delta    sigma   weight residual
    1.516  1.458  0.058 2.50e-02 1.60e+03 5.42e+00
  bond pdb=" CB  ASN A 190 "
       pdb=" CG  ASN A 190 "
    ideal  model  delta    sigma   weight residual
    1.516  1.458  0.058 2.50e-02 1.60e+03 5.41e+00
  ... (remaining 9835 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 12746
        2.83 -     5.66: 522
        5.66 -     8.50: 115
        8.50 -    11.33: 9
       11.33 -    14.16: 9
  Bond angle restraints: 13401
  Sorted by residual:
  angle pdb=" C   LEU A 409 "
        pdb=" N   ASP A 410 "
        pdb=" CA  ASP A 410 "
      ideal   model   delta    sigma   weight residual
     121.54  129.88   -8.34 1.91e+00 2.74e-01 1.91e+01
  angle pdb=" C   LEU C 409 "
        pdb=" N   ASP C 410 "
        pdb=" CA  ASP C 410 "
      ideal   model   delta    sigma   weight residual
     121.54  129.87   -8.33 1.91e+00 2.74e-01 1.90e+01
  angle pdb=" C   LEU B 409 "
        pdb=" N   ASP B 410 "
        pdb=" CA  ASP B 410 "
      ideal   model   delta    sigma   weight residual
     121.54  129.80   -8.26 1.91e+00 2.74e-01 1.87e+01
  angle pdb=" CA  LEU A 321 "
        pdb=" CB  LEU A 321 "
        pdb=" CG  LEU A 321 "
      ideal   model   delta    sigma   weight residual
     116.30  130.46  -14.16 3.50e+00 8.16e-02 1.64e+01
  angle pdb=" CA  LEU B 321 "
        pdb=" CB  LEU B 321 "
        pdb=" CG  LEU B 321 "
      ideal   model   delta    sigma   weight residual
     116.30  130.46  -14.16 3.50e+00 8.16e-02 1.64e+01
  ... (remaining 13396 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.74: 5141
       15.74 -    31.49: 454
       31.49 -    47.23: 165
       47.23 -    62.97: 21
       62.97 -    78.71: 9
  Dihedral angle restraints: 5790
    sinusoidal: 2127
      harmonic: 3663
  Sorted by residual:
  dihedral pdb=" CA  ALA C 123 "
           pdb=" C   ALA C 123 "
           pdb=" N   LEU C 124 "
           pdb=" CA  LEU C 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.26  -31.74     0      5.00e+00 4.00e-02 4.03e+01
  dihedral pdb=" CA  ALA B 123 "
           pdb=" C   ALA B 123 "
           pdb=" N   LEU B 124 "
           pdb=" CA  LEU B 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.26  -31.74     0      5.00e+00 4.00e-02 4.03e+01
  dihedral pdb=" CA  ALA A 123 "
           pdb=" C   ALA A 123 "
           pdb=" N   LEU A 124 "
           pdb=" CA  LEU A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.28  -31.72     0      5.00e+00 4.00e-02 4.02e+01
  ... (remaining 5787 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1209
       0.071 -    0.143: 392
       0.143 -    0.214: 60
       0.214 -    0.286: 10
       0.286 -    0.357: 6
  Chirality restraints: 1677
  Sorted by residual:
  chirality pdb=" CA  ASP B 410 "
            pdb=" N   ASP B 410 "
            pdb=" C   ASP B 410 "
            pdb=" CB  ASP B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  ASP C 410 "
            pdb=" N   ASP C 410 "
            pdb=" C   ASP C 410 "
            pdb=" CB  ASP C 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CA  ASP A 410 "
            pdb=" N   ASP A 410 "
            pdb=" C   ASP A 410 "
            pdb=" CB  ASP A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.10e+00
  ... (remaining 1674 not shown)

  Planarity restraints: 1665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 321 "    0.044 5.00e-02 4.00e+02   6.55e-02 6.85e+00
        pdb=" N   PRO A 322 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 379 "    0.044 5.00e-02 4.00e+02   6.54e-02 6.84e+00
        pdb=" N   PRO C 380 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 380 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 380 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 321 "    0.044 5.00e-02 4.00e+02   6.54e-02 6.84e+00
        pdb=" N   PRO C 322 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 322 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 322 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1662 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 3288
        2.84 -     3.36: 10139
        3.36 -     3.87: 15988
        3.87 -     4.39: 18808
        4.39 -     4.90: 29440
  Nonbonded interactions: 77663
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 227 "
            pdb=" NH2 ARG C 202 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" O   LEU C 119 "
            pdb=" NH1 ARG C 246 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   LEU B 119 "
            pdb=" NH1 ARG B 246 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   LEU A 119 "
            pdb=" NH1 ARG A 246 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   LYS A 372 "
            pdb=" OG  SER A 375 "
     model   vdw
     2.335 3.040
  ... (remaining 77658 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.950
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
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      :  0.012   0.140   9840  Z= 0.752
  Angle     :  1.401  14.161  13401  Z= 0.698
  Chirality :  0.072   0.357   1677
  Planarity :  0.008   0.065   1665
  Dihedral  : 14.504  78.713   3438
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.84 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 16.42 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -6.53 (0.15), residues: 1284
  helix: -4.40 (0.08), residues: 879
  sheet: -3.60 (0.50), residues: 60
  loop : -3.38 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 275 
 HIS   0.006   0.002   HIS C 316 
 PHE   0.023   0.003   PHE B 201 
 TYR   0.023   0.004   TYR C 485 
 ARG   0.004   0.001   ARG A 330 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 300
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 TRP cc_start: 0.7754 (m100) cc_final: 0.7465 (m100)
REVERT: A  248 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9065 (tt)
REVERT: A  473 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: B  130 TRP cc_start: 0.7843 (m100) cc_final: 0.7607 (m100)
REVERT: B  181 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7869 (mp)
REVERT: B  263 ASN cc_start: 0.8929 (p0) cc_final: 0.8709 (p0)
REVERT: B  483 GLN cc_start: 0.7767 (pp30) cc_final: 0.6904 (pp30)
REVERT: C  130 TRP cc_start: 0.7865 (m100) cc_final: 0.7505 (m100)
REVERT: C  186 ASP cc_start: 0.8724 (t70) cc_final: 0.8496 (t0)
REVERT: C  275 TRP cc_start: 0.8221 (m100) cc_final: 0.7533 (m-10)
REVERT: C  483 GLN cc_start: 0.7831 (pp30) cc_final: 0.7278 (pp30)
  outliers start: 57
  outliers final: 18
  residues processed: 324
  average time/residue: 0.1996
  time to fit residues: 92.4900
Evaluate side-chains
  235 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 215
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain C residue  320 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0060
   chunk 61 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    1.3000

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
A 316 HIS
A 367 ASN
A 373 HIS
A 386 ASN
A 403 GLN
A 484 ASN
B 154 GLN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 367 ASN
B 373 HIS
B 403 GLN
** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 154 GLN
C 316 HIS
C 367 ASN
C 386 ASN
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 484 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.112421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.088071 restraints weight = 20462.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.087038 restraints weight = 23963.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.088025 restraints weight = 21777.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9840  Z= 0.249
  Angle     :  0.840  14.432  13401  Z= 0.406
  Chirality :  0.045   0.202   1677
  Planarity :  0.006   0.045   1665
  Dihedral  :  7.452  57.682   1403
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 18.67 %
    Favored  : 73.70 %
  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: -4.59 (0.19), residues: 1284
  helix: -2.92 (0.13), residues: 888
  sheet: -3.58 (0.52), residues: 60
  loop : -2.52 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 461 
 HIS   0.005   0.002   HIS A 316 
 PHE   0.031   0.002   PHE B 400 
 TYR   0.019   0.002   TYR A 276 
 ARG   0.003   0.001   ARG C 189 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 278
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8162 (tm)
REVERT: A   91 PHE cc_start: 0.8905 (t80) cc_final: 0.8683 (t80)
REVERT: A  132 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8586 (tt)
REVERT: A  246 ARG cc_start: 0.8257 (tmm-80) cc_final: 0.7973 (tmm-80)
REVERT: A  248 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9069 (tt)
REVERT: A  256 ILE cc_start: 0.9254 (mp) cc_final: 0.9025 (mp)
REVERT: A  311 LEU cc_start: 0.9373 (tp) cc_final: 0.9135 (tt)
REVERT: A  331 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8606 (mmmt)
REVERT: A  392 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9137 (mm)
REVERT: B  149 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8647 (tp)
REVERT: B  247 LYS cc_start: 0.8179 (tttt) cc_final: 0.7897 (ttmt)
REVERT: C  275 TRP cc_start: 0.8132 (m100) cc_final: 0.7392 (m-10)
REVERT: C  387 MET cc_start: 0.8328 (mtp) cc_final: 0.8011 (mtp)
REVERT: C  388 ASP cc_start: 0.8754 (m-30) cc_final: 0.8501 (m-30)
REVERT: C  413 LYS cc_start: 0.9107 (ttmp) cc_final: 0.8888 (ttpt)
REVERT: C  482 LEU cc_start: 0.8871 (mm) cc_final: 0.8670 (mm)
  outliers start: 78
  outliers final: 26
  residues processed: 335
  average time/residue: 0.2108
  time to fit residues: 104.1035
Evaluate side-chains
  259 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 228
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  392 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 34 optimal weight:    0.7980
   chunk 113 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0170
   chunk 77 optimal weight:    7.9990
   chunk 86 optimal weight:   20.0000
   chunk 124 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 76 optimal weight:    0.0570
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
C 386 ASN
C 394 GLN
C 484 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.115649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.092593 restraints weight = 21090.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.092152 restraints weight = 23937.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.092879 restraints weight = 22188.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9840  Z= 0.198
  Angle     :  0.844  14.531  13401  Z= 0.383
  Chirality :  0.044   0.190   1677
  Planarity :  0.005   0.042   1665
  Dihedral  :  6.382  55.122   1384
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 23.75 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.59 (0.21), residues: 1284
  helix: -2.22 (0.15), residues: 870
  sheet: -3.35 (0.57), residues: 60
  loop : -1.98 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 461 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.031   0.002   PHE B 400 
 TYR   0.029   0.002   TYR C 305 
 ARG   0.002   0.000   ARG C 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 263
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8017 (tm)
REVERT: A  132 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8571 (tt)
REVERT: A  149 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7905 (tp)
REVERT: A  246 ARG cc_start: 0.8191 (tmm-80) cc_final: 0.7936 (tmm-80)
REVERT: A  473 GLU cc_start: 0.8098 (tt0) cc_final: 0.7831 (tm-30)
REVERT: B  149 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8247 (tp)
REVERT: B  247 LYS cc_start: 0.8289 (tttt) cc_final: 0.7893 (ttmt)
REVERT: C  275 TRP cc_start: 0.7945 (m100) cc_final: 0.7647 (m-10)
REVERT: C  305 TYR cc_start: 0.8777 (t80) cc_final: 0.8500 (t80)
REVERT: C  601 GLN cc_start: 0.7626 (pm20) cc_final: 0.7292 (pm20)
  outliers start: 73
  outliers final: 29
  residues processed: 310
  average time/residue: 0.1791
  time to fit residues: 82.7476
Evaluate side-chains
  264 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 231
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  457 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0470
   chunk 117 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.8882

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

Flipped N/Q/H residues before XYZ refinement:
C 394 GLN
C 407 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.114427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.090232 restraints weight = 20886.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.089762 restraints weight = 22495.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.090330 restraints weight = 18492.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9840  Z= 0.211
  Angle     :  0.843  15.077  13401  Z= 0.382
  Chirality :  0.045   0.255   1677
  Planarity :  0.004   0.040   1665
  Dihedral  :  5.563  31.587   1378
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 25.32 %
    Favored  : 67.84 %
  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: -3.05 (0.22), residues: 1284
  helix: -1.90 (0.16), residues: 882
  sheet: -3.19 (0.59), residues: 60
  loop : -1.47 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 461 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.025   0.001   PHE A 400 
 TYR   0.018   0.001   TYR C 305 
 ARG   0.002   0.000   ARG C 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 246
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7935 (tt)
REVERT: A  132 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8610 (tt)
REVERT: A  149 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8132 (tp)
REVERT: A  246 ARG cc_start: 0.8259 (tmm-80) cc_final: 0.8010 (tmm-80)
REVERT: A  323 LEU cc_start: 0.8897 (tt) cc_final: 0.8679 (tt)
REVERT: A  392 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9166 (mm)
REVERT: B  149 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8387 (tp)
REVERT: B  455 LEU cc_start: 0.8456 (pt) cc_final: 0.8205 (pt)
REVERT: C  283 PHE cc_start: 0.8292 (m-80) cc_final: 0.8088 (m-80)
REVERT: C  305 TYR cc_start: 0.8780 (t80) cc_final: 0.8460 (t80)
REVERT: C  361 MET cc_start: 0.6975 (mpp) cc_final: 0.6734 (mpp)
REVERT: C  413 LYS cc_start: 0.9038 (ttmp) cc_final: 0.8831 (ttpt)
  outliers start: 70
  outliers final: 36
  residues processed: 295
  average time/residue: 0.1691
  time to fit residues: 73.7859
Evaluate side-chains
  264 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 223
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 TRP
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain C residue  392 LEU
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  473 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 103 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 128 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
C 394 GLN
C 407 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.107743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.083527 restraints weight = 20549.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.082772 restraints weight = 22076.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.083504 restraints weight = 20320.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   9840  Z= 0.293
  Angle     :  0.868  14.271  13401  Z= 0.398
  Chirality :  0.047   0.221   1677
  Planarity :  0.004   0.039   1665
  Dihedral  :  5.565  32.973   1376
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 25.81 %
    Favored  : 67.45 %
  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: -2.74 (0.22), residues: 1284
  helix: -1.64 (0.16), residues: 897
  sheet: -3.25 (0.58), residues: 60
  loop : -1.35 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 461 
 HIS   0.005   0.001   HIS B 316 
 PHE   0.021   0.002   PHE A 400 
 TYR   0.014   0.002   TYR C 305 
 ARG   0.002   0.000   ARG B 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 235
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9111 (t)
REVERT: A  132 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8708 (tt)
REVERT: A  149 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8344 (tp)
REVERT: A  334 TYR cc_start: 0.6639 (m-80) cc_final: 0.6310 (m-10)
REVERT: A  392 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9195 (mm)
REVERT: B   90 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.8885 (t)
REVERT: B  149 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8673 (tp)
REVERT: B  341 VAL cc_start: 0.8460 (t) cc_final: 0.8178 (p)
REVERT: B  444 GLU cc_start: 0.7575 (tp30) cc_final: 0.7269 (tp30)
REVERT: B  455 LEU cc_start: 0.8701 (pt) cc_final: 0.8464 (pt)
REVERT: C   90 VAL cc_start: 0.9403 (OUTLIER) cc_final: 0.9154 (p)
REVERT: C  112 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9014 (tt)
REVERT: C  305 TYR cc_start: 0.9010 (t80) cc_final: 0.8684 (t80)
REVERT: C  320 VAL cc_start: 0.8832 (m) cc_final: 0.8544 (p)
REVERT: C  461 TRP cc_start: 0.9050 (p-90) cc_final: 0.8805 (p-90)
REVERT: C  470 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9042 (tt)
  outliers start: 69
  outliers final: 37
  residues processed: 283
  average time/residue: 0.1770
  time to fit residues: 74.0665
Evaluate side-chains
  261 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 215
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  275 TRP
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  392 LEU
Chi-restraints excluded: chain C residue  415 ILE
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  470 LEU
Chi-restraints excluded: chain C residue  473 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0170
   chunk 65 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 85 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
** A 313 HIS ** 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 = 0.3479 r_free = 0.3479 target = 0.111159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.086931 restraints weight = 20643.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.085943 restraints weight = 22379.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.086452 restraints weight = 20168.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9840  Z= 0.207
  Angle     :  0.872  14.678  13401  Z= 0.390
  Chirality :  0.047   0.287   1677
  Planarity :  0.004   0.036   1665
  Dihedral  :  5.319  31.697   1376
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 26.88 %
    Favored  : 67.16 %
  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: -2.52 (0.23), residues: 1284
  helix: -1.46 (0.16), residues: 894
  sheet: -3.05 (0.60), residues: 60
  loop : -1.36 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 461 
 HIS   0.003   0.001   HIS B 373 
 PHE   0.020   0.001   PHE A 400 
 TYR   0.012   0.001   TYR C 305 
 ARG   0.003   0.000   ARG B 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 249
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 PHE cc_start: 0.7101 (m-80) cc_final: 0.6178 (m-80)
REVERT: A   90 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9075 (t)
REVERT: A  132 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8610 (tt)
REVERT: A  246 ARG cc_start: 0.8316 (tmm-80) cc_final: 0.7916 (tmm-80)
REVERT: A  268 VAL cc_start: 0.9007 (p) cc_final: 0.8659 (t)
REVERT: A  334 TYR cc_start: 0.6417 (m-80) cc_final: 0.6170 (m-10)
REVERT: B   90 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.8846 (t)
REVERT: B  149 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8463 (tp)
REVERT: B  341 VAL cc_start: 0.8395 (t) cc_final: 0.8065 (p)
REVERT: B  387 MET cc_start: 0.8043 (mtt) cc_final: 0.7675 (mtm)
REVERT: B  444 GLU cc_start: 0.7477 (tp30) cc_final: 0.7214 (tp30)
REVERT: C  323 LEU cc_start: 0.8790 (tt) cc_final: 0.8569 (mp)
REVERT: C  387 MET cc_start: 0.8104 (mtp) cc_final: 0.7844 (mtp)
REVERT: C  388 ASP cc_start: 0.8528 (m-30) cc_final: 0.8288 (m-30)
REVERT: C  461 TRP cc_start: 0.8988 (p-90) cc_final: 0.8739 (p-90)
  outliers start: 61
  outliers final: 40
  residues processed: 286
  average time/residue: 0.1769
  time to fit residues: 74.5122
Evaluate side-chains
  269 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 225
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 TRP
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  473 GLU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  473 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 11 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0040
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0050
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.4408

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

Flipped N/Q/H residues before XYZ refinement:
** A 471 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 = 0.3506 r_free = 0.3506 target = 0.112802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.089071 restraints weight = 20685.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.088615 restraints weight = 22174.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.089433 restraints weight = 21058.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.4649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9840  Z= 0.205
  Angle     :  0.892  14.776  13401  Z= 0.395
  Chirality :  0.046   0.235   1677
  Planarity :  0.004   0.035   1665
  Dihedral  :  5.168  31.177   1376
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 28.64 %
    Favored  : 64.91 %
  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: -2.44 (0.23), residues: 1284
  helix: -1.35 (0.16), residues: 903
  sheet: -2.87 (0.61), residues: 60
  loop : -1.51 (0.37), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 461 
 HIS   0.002   0.001   HIS C 316 
 PHE   0.025   0.001   PHE B 328 
 TYR   0.018   0.001   TYR A 325 
 ARG   0.003   0.000   ARG B 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 239
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 PHE cc_start: 0.6890 (m-80) cc_final: 0.6136 (m-80)
REVERT: A   90 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8982 (t)
REVERT: A  132 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8582 (tt)
REVERT: A  246 ARG cc_start: 0.8255 (tmm-80) cc_final: 0.7870 (tmm-80)
REVERT: A  387 MET cc_start: 0.7535 (mtp) cc_final: 0.7168 (mtm)
REVERT: B  149 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8440 (tp)
REVERT: B  387 MET cc_start: 0.7999 (mtt) cc_final: 0.7732 (mtm)
REVERT: B  413 LYS cc_start: 0.8944 (ttmp) cc_final: 0.8717 (ttmt)
REVERT: B  455 LEU cc_start: 0.8375 (pt) cc_final: 0.8162 (pt)
REVERT: C   89 PHE cc_start: 0.6950 (m-80) cc_final: 0.6377 (m-80)
REVERT: C   90 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.9015 (t)
REVERT: C  323 LEU cc_start: 0.8757 (tt) cc_final: 0.8528 (mp)
REVERT: C  387 MET cc_start: 0.8068 (mtp) cc_final: 0.7768 (mtp)
REVERT: C  388 ASP cc_start: 0.8526 (m-30) cc_final: 0.8196 (m-30)
REVERT: C  461 TRP cc_start: 0.8937 (p-90) cc_final: 0.8719 (p-90)
REVERT: C  470 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8837 (tt)
  outliers start: 66
  outliers final: 41
  residues processed: 285
  average time/residue: 0.1774
  time to fit residues: 74.3167
Evaluate side-chains
  274 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 228
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 TRP
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  226 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  342 THR
Chi-restraints excluded: chain C residue  392 LEU
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  470 LEU
Chi-restraints excluded: chain C residue  473 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 127 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 62 optimal weight:    0.0980
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 407 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.112783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.087908 restraints weight = 20668.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.087843 restraints weight = 20376.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.088551 restraints weight = 16134.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9840  Z= 0.219
  Angle     :  0.894  14.658  13401  Z= 0.398
  Chirality :  0.047   0.272   1677
  Planarity :  0.004   0.034   1665
  Dihedral  :  4.992  30.798   1373
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 29.33 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.23), residues: 1284
  helix: -1.27 (0.16), residues: 903
  sheet: -2.79 (0.61), residues: 60
  loop : -1.48 (0.37), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 461 
 HIS   0.003   0.001   HIS C 316 
 PHE   0.041   0.002   PHE B 400 
 TYR   0.012   0.001   TYR C 305 
 ARG   0.003   0.000   ARG B 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 240
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 PHE cc_start: 0.6878 (m-80) cc_final: 0.6178 (m-80)
REVERT: A   90 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8959 (t)
REVERT: A  132 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8587 (tt)
REVERT: A  246 ARG cc_start: 0.8151 (tmm-80) cc_final: 0.7810 (tmm-80)
REVERT: B  149 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (tp)
REVERT: B  387 MET cc_start: 0.7967 (mtt) cc_final: 0.7752 (mtm)
REVERT: B  413 LYS cc_start: 0.8906 (ttmp) cc_final: 0.8706 (ttmt)
REVERT: C   89 PHE cc_start: 0.6886 (m-80) cc_final: 0.6361 (m-80)
REVERT: C   90 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8960 (t)
REVERT: C  387 MET cc_start: 0.8022 (mtp) cc_final: 0.7740 (mtp)
REVERT: C  388 ASP cc_start: 0.8492 (m-30) cc_final: 0.8172 (m-30)
REVERT: C  470 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8824 (tt)
  outliers start: 55
  outliers final: 40
  residues processed: 278
  average time/residue: 0.1836
  time to fit residues: 74.2721
Evaluate side-chains
  268 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 223
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 TRP
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  342 THR
Chi-restraints excluded: chain C residue  392 LEU
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  470 LEU
Chi-restraints excluded: chain C residue  473 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0970
   chunk 128 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 403 GLN
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 403 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.111345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.085831 restraints weight = 20466.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.085991 restraints weight = 19638.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.086764 restraints weight = 15308.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.4825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9840  Z= 0.249
  Angle     :  0.908  14.306  13401  Z= 0.410
  Chirality :  0.048   0.261   1677
  Planarity :  0.004   0.036   1665
  Dihedral  :  5.036  31.197   1373
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 30.01 %
    Favored  : 64.81 %
  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: -2.23 (0.23), residues: 1284
  helix: -1.19 (0.16), residues: 897
  sheet: -2.75 (0.62), residues: 60
  loop : -1.45 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP C 461 
 HIS   0.003   0.001   HIS C 316 
 PHE   0.060   0.002   PHE B 400 
 TYR   0.009   0.001   TYR C 305 
 ARG   0.002   0.000   ARG B 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 234
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 PHE cc_start: 0.6888 (m-80) cc_final: 0.6172 (m-80)
REVERT: A   90 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9052 (t)
REVERT: A  132 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8632 (tt)
REVERT: A  246 ARG cc_start: 0.8296 (tmm-80) cc_final: 0.7902 (tmm-80)
REVERT: B  341 VAL cc_start: 0.8482 (t) cc_final: 0.8218 (p)
REVERT: B  387 MET cc_start: 0.8159 (mtt) cc_final: 0.7937 (mtm)
REVERT: B  400 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8421 (t80)
REVERT: B  413 LYS cc_start: 0.8929 (ttmp) cc_final: 0.8711 (ttmt)
REVERT: C   89 PHE cc_start: 0.6989 (m-80) cc_final: 0.6361 (m-80)
REVERT: C   90 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9025 (t)
REVERT: C  388 ASP cc_start: 0.8632 (m-30) cc_final: 0.8349 (m-30)
REVERT: C  470 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9037 (tt)
  outliers start: 53
  outliers final: 43
  residues processed: 271
  average time/residue: 0.1800
  time to fit residues: 71.3123
Evaluate side-chains
  271 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 223
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 TRP
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  400 PHE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  232 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  342 THR
Chi-restraints excluded: chain C residue  392 LEU
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  470 LEU
Chi-restraints excluded: chain C residue  473 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 118 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 105 optimal weight:    0.3980
   chunk 28 optimal weight:    0.4980
   chunk 98 optimal weight:    3.9990
   chunk 86 optimal weight:   20.0000
   chunk 94 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 403 GLN
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 GLN
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 403 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.115020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.089773 restraints weight = 20858.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.089933 restraints weight = 16464.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.090398 restraints weight = 14353.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   9840  Z= 0.238
  Angle     :  0.931  14.586  13401  Z= 0.415
  Chirality :  0.048   0.304   1677
  Planarity :  0.004   0.037   1665
  Dihedral  :  4.998  31.195   1373
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 31.18 %
    Favored  : 64.22 %
  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: -2.22 (0.23), residues: 1284
  helix: -1.18 (0.16), residues: 900
  sheet: -2.57 (0.63), residues: 60
  loop : -1.49 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 461 
 HIS   0.003   0.001   HIS A 316 
 PHE   0.060   0.002   PHE B 400 
 TYR   0.011   0.001   TYR C 305 
 ARG   0.003   0.000   ARG B 246 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 223
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 PHE cc_start: 0.6902 (m-80) cc_final: 0.6147 (m-80)
REVERT: A   90 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9087 (t)
REVERT: A  132 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8672 (tt)
REVERT: A  246 ARG cc_start: 0.8356 (tmm-80) cc_final: 0.7929 (tmm-80)
REVERT: A  292 MET cc_start: 0.6330 (mmt) cc_final: 0.6083 (mmm)
REVERT: A  362 LYS cc_start: 0.8120 (tptt) cc_final: 0.7812 (tppt)
REVERT: A  387 MET cc_start: 0.7594 (mtp) cc_final: 0.7082 (mtm)
REVERT: B  387 MET cc_start: 0.8137 (mtt) cc_final: 0.7825 (mtm)
REVERT: B  413 LYS cc_start: 0.8940 (ttmp) cc_final: 0.8726 (ttmt)
REVERT: C   89 PHE cc_start: 0.7038 (m-80) cc_final: 0.6345 (m-80)
REVERT: C   90 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9064 (t)
REVERT: C  387 MET cc_start: 0.8146 (mtp) cc_final: 0.7836 (mtp)
REVERT: C  388 ASP cc_start: 0.8658 (m-30) cc_final: 0.8364 (m-30)
REVERT: C  470 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9041 (tt)
  outliers start: 47
  outliers final: 39
  residues processed: 255
  average time/residue: 0.1836
  time to fit residues: 68.4524
Evaluate side-chains
  261 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 218
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 TRP
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  337 LEU
Chi-restraints excluded: chain C residue  392 LEU
Chi-restraints excluded: chain C residue  457 LEU
Chi-restraints excluded: chain C residue  470 LEU
Chi-restraints excluded: chain C residue  473 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 117 optimal weight:    0.0970
   chunk 123 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:   20.0000
   overall best weight:    0.8178

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

Flipped N/Q/H residues before XYZ refinement:
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 GLN
B 407 GLN
C 403 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.112827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.087554 restraints weight = 20527.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.087700 restraints weight = 18096.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.088061 restraints weight = 15503.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9840  Z= 0.226
  Angle     :  0.936  14.595  13401  Z= 0.415
  Chirality :  0.048   0.297   1677
  Planarity :  0.004   0.038   1665
  Dihedral  :  4.953  31.193   1373
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 31.28 %
    Favored  : 64.03 %
  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: -2.09 (0.23), residues: 1284
  helix: -1.09 (0.17), residues: 900
  sheet: -2.51 (0.63), residues: 60
  loop : -1.45 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 461 
 HIS   0.003   0.001   HIS A 316 
 PHE   0.033   0.001   PHE A 400 
 TYR   0.014   0.001   TYR A 325 
 ARG   0.003   0.000   ARG B 246 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3290.19 seconds
wall clock time: 58 minutes 44.90 seconds (3524.90 seconds total)