Starting phenix.real_space_refine
on Tue Feb 11 13:00:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzv_41770/02_2025/8tzv_41770.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzv_41770/02_2025/8tzv_41770.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzv_41770/02_2025/8tzv_41770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzv_41770/02_2025/8tzv_41770.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzv_41770/02_2025/8tzv_41770.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzv_41770/02_2025/8tzv_41770.cif"
  }
  resolution = 2.8
  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=   0.002 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      44      5.16       5
     C    3634      2.51       5
     N     948      2.21       5
     O    1052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5680
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2839
          Classifications: {'peptide': 348}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 322}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2839
          Classifications: {'peptide': 348}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 322}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    138  SG  CYS A  23      22.992  26.367  78.483  1.00205.25           S
  ATOM    160  SG  CYS A  26      20.287  26.051  79.798  1.00196.05           S
  ATOM    528  SG  CYS A  71      19.264  28.175  79.875  1.00207.19           S
  ATOM    534  SG  CYS A  72      23.034  28.417  80.130  1.00186.79           S
  ATOM   2977  SG  CYS B  23      23.388  44.045  32.883  1.00220.55           S
  ATOM   2999  SG  CYS B  26      21.848  44.317  31.167  1.00214.45           S
  ATOM   3367  SG  CYS B  71      20.232  42.218  31.374  1.00209.17           S
  ATOM   3373  SG  CYS B  72      23.292  42.074  29.559  1.00201.96           S

  Time building chain proxies: 3.93, per 1000 atoms: 0.69
  Number of scatterers: 5680
  At special positions: 0
  Unit cell: (75.04, 69.68, 111.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      44     16.00
     O    1052      8.00
     N     948      7.00
     C    3634      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 640.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 600 "
        pdb="ZN    ZN A 600 " - pdb=" SG  CYS A  23 "
        pdb="ZN    ZN A 600 " - pdb=" SG  CYS A  71 "
        pdb="ZN    ZN A 600 " - pdb=" SG  CYS A  26 "
        pdb="ZN    ZN A 600 " - pdb=" SG  CYS A  72 "
      pdb="  ZN B 600 "
        pdb="ZN    ZN B 600 " - pdb=" SG  CYS B  26 "
        pdb="ZN    ZN B 600 " - pdb=" SG  CYS B  72 "
        pdb="ZN    ZN B 600 " - pdb=" SG  CYS B  71 "
        pdb="ZN    ZN B 600 " - pdb=" SG  CYS B  23 "
      Number of angles added : 12


  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      39.8% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 52
    Processing helix  chain 'A' and resid 87 through 102
    Processing helix  chain 'A' and resid 281 through 287
    Processing helix  chain 'A' and resid 287 through 302
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 311 through 320
    Processing helix  chain 'A' and resid 372 through 375
    Processing helix  chain 'A' and resid 378 through 396
      removed outlier: 3.853A  pdb=" N   ALA A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 448
      Proline residue:  A 443  - end of helix
    Processing helix  chain 'A' and resid 467 through 470
    Processing helix  chain 'A' and resid 482 through 487
      removed outlier: 4.110A  pdb=" N   LYS A 487 " --> pdb=" O   GLY A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 511
      removed outlier: 3.793A  pdb=" N   GLU A 495 " --> pdb=" O   ASP A 491 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   GLN A 507 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      removed outlier: 9.708A  pdb=" N   LYS A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   CYS A 509 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU A 511 " --> pdb=" O   GLN A 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 53
      removed outlier: 3.911A  pdb=" N   ASP B  49 " --> pdb=" O   GLN B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 84
      removed outlier: 3.652A  pdb=" N   PHE B  84 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 84'
    Processing helix  chain 'B' and resid 87 through 104
    Processing helix  chain 'B' and resid 281 through 287
    Processing helix  chain 'B' and resid 287 through 302
    Processing helix  chain 'B' and resid 306 through 310
    Processing helix  chain 'B' and resid 311 through 320
    Processing helix  chain 'B' and resid 372 through 377
      removed outlier: 4.646A  pdb=" N   PHE B 376 " --> pdb=" O   ASP B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 398
      removed outlier: 3.716A  pdb=" N   TYR B 382 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LYS B 397 " --> pdb=" O   GLN B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 441 through 446
      removed outlier: 3.624A  pdb=" N   LEU B 445 " --> pdb=" O   CYS B 441 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLU B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 441 through 446'
    Processing helix  chain 'B' and resid 467 through 470
    Processing helix  chain 'B' and resid 482 through 489
    Processing helix  chain 'B' and resid 494 through 512
      removed outlier: 3.901A  pdb=" N   VAL B 498 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   GLN B 507 " --> pdb=" O   SER B 503 " (cutoff:3.500A)
      removed outlier: 8.806A  pdb=" N   LYS B 508 " --> pdb=" O   LEU B 504 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   CYS B 509 " --> pdb=" O   VAL B 505 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG B 512 " --> pdb=" O   LYS B 508 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57
      removed outlier: 3.600A  pdb=" N   GLY A  36 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   VAL A  11 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   SER A  10 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405
    Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 276
      removed outlier: 6.674A  pdb=" N   GLY A 338 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   ASP A 357 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   PHE A 340 " --> pdb=" O   VAL A 355 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   VAL A 355 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLN A 342 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   VAL A 353 " --> pdb=" O   GLN A 342 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   TYR A 344 " --> pdb=" O   ILE A 351 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   TYR A 367 " --> pdb=" O   VAL A 355 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ASP A 357 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   SER A 365 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57
      removed outlier: 5.262A  pdb=" N   MET B  37 " --> pdb=" O   PHE B  15 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   PHE B  15 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   ALA B  39 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   ASP B  13 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   GLN B 472 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 270 through 276
      removed outlier: 4.043A  pdb=" N   ALA B 352 " --> pdb=" O   TYR B 344 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   LEU B 346 " --> pdb=" O   ILE B 350 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   ILE B 350 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ASP B 357 " --> pdb=" O   SER B 365 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   SER B 365 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B 363 " --> pdb=" O   TYR B 405 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY B 407 " --> pdb=" O   VAL B 363 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   SER B 365 " --> pdb=" O   GLY B 407 " (cutoff:3.500A)
      removed outlier: 9.833A  pdb=" N   TYR B 409 " --> pdb=" O   SER B 365 " (cutoff:3.500A)
      removed outlier: 15.313A  pdb=" N   TYR B 367 " --> pdb=" O   TYR B 409 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ILE B  77 " --> pdb=" O   MET B 406 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   PHE B 408 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   TYR B  75 " --> pdb=" O   PHE B 408 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   THR B  76 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    600 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1794
        1.34 -     1.46: 1391
        1.46 -     1.58: 2597
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 5842
  Sorted by residual:
  bond pdb=" CA  VAL A  66 "
       pdb=" CB  VAL A  66 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.010 1.11e-02 8.12e+03 7.34e-01
  bond pdb=" CA  VAL B 277 "
       pdb=" CB  VAL B 277 "
    ideal  model  delta    sigma   weight residual
    1.528  1.539 -0.011 1.34e-02 5.57e+03 6.65e-01
  bond pdb=" CA  GLY A  59 "
       pdb=" C   GLY A  59 "
    ideal  model  delta    sigma   weight residual
    1.514  1.523 -0.008 1.41e-02 5.03e+03 3.44e-01
  bond pdb=" CA  PRO B 443 "
       pdb=" C   PRO B 443 "
    ideal  model  delta    sigma   weight residual
    1.528  1.521  0.007 1.20e-02 6.94e+03 3.24e-01
  bond pdb=" CA  LEU A 442 "
       pdb=" C   LEU A 442 "
    ideal  model  delta    sigma   weight residual
    1.520  1.526 -0.006 1.23e-02 6.61e+03 2.46e-01
  ... (remaining 5837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 7699
        0.95 -     1.89: 137
        1.89 -     2.84: 38
        2.84 -     3.79: 26
        3.79 -     4.74: 2
  Bond angle restraints: 7902
  Sorted by residual:
  angle pdb=" C   LEU B 442 "
        pdb=" N   PRO B 443 "
        pdb=" CA  PRO B 443 "
      ideal   model   delta    sigma   weight residual
     121.91  118.95    2.96 1.35e+00 5.49e-01 4.79e+00
  angle pdb=" N   VAL B 277 "
        pdb=" CA  VAL B 277 "
        pdb=" C   VAL B 277 "
      ideal   model   delta    sigma   weight residual
     106.32  109.71   -3.39 1.61e+00 3.86e-01 4.43e+00
  angle pdb=" C   ILE A 479 "
        pdb=" N   MET A 480 "
        pdb=" CA  MET A 480 "
      ideal   model   delta    sigma   weight residual
     122.74  119.25    3.49 2.44e+00 1.68e-01 2.05e+00
  angle pdb=" CA  PRO A   9 "
        pdb=" C   PRO A   9 "
        pdb=" N   SER A  10 "
      ideal   model   delta    sigma   weight residual
     114.75  116.68   -1.93 1.45e+00 4.76e-01 1.78e+00
  angle pdb=" C   ARG A 423 "
        pdb=" CA  ARG A 423 "
        pdb=" CB  ARG A 423 "
      ideal   model   delta    sigma   weight residual
     108.91  111.01   -2.10 1.65e+00 3.67e-01 1.62e+00
  ... (remaining 7897 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.83: 3279
       10.83 -    21.66: 186
       21.66 -    32.49: 51
       32.49 -    43.32: 13
       43.32 -    54.15: 3
  Dihedral angle restraints: 3532
    sinusoidal: 1466
      harmonic: 2066
  Sorted by residual:
  dihedral pdb=" N   TYR A 485 "
           pdb=" CA  TYR A 485 "
           pdb=" CB  TYR A 485 "
           pdb=" CG  TYR A 485 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.15  -54.15     3      1.50e+01 4.44e-03 9.26e+00
  dihedral pdb=" N   ARG A  33 "
           pdb=" CA  ARG A  33 "
           pdb=" CB  ARG A  33 "
           pdb=" CG  ARG A  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.29  -52.71     3      1.50e+01 4.44e-03 9.14e+00
  dihedral pdb=" CA  ARG A  33 "
           pdb=" CB  ARG A  33 "
           pdb=" CG  ARG A  33 "
           pdb=" CD  ARG A  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -134.43  -45.57     3      1.50e+01 4.44e-03 8.19e+00
  ... (remaining 3529 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 434
       0.025 -    0.050: 233
       0.050 -    0.074: 73
       0.074 -    0.099: 39
       0.099 -    0.124: 23
  Chirality restraints: 802
  Sorted by residual:
  chirality pdb=" CA  ILE A 479 "
            pdb=" N   ILE A 479 "
            pdb=" C   ILE A 479 "
            pdb=" CB  ILE A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  ILE B 479 "
            pdb=" N   ILE B 479 "
            pdb=" C   ILE B 479 "
            pdb=" CB  ILE B 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.69e-01
  chirality pdb=" CA  VAL A  62 "
            pdb=" N   VAL A  62 "
            pdb=" C   VAL A  62 "
            pdb=" CB  VAL A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.53e-01
  ... (remaining 799 not shown)

  Planarity restraints: 1024
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 442 "   -0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO B 443 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 443 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 443 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 456 "   -0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO A 457 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 457 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 457 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 491 "   -0.016 5.00e-02 4.00e+02   2.42e-02 9.36e-01
        pdb=" N   PRO B 492 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO B 492 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 492 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 1021 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 350
        2.74 -     3.28: 5618
        3.28 -     3.82: 9529
        3.82 -     4.36: 11107
        4.36 -     4.90: 19281
  Nonbonded interactions: 45885
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 387 "
            pdb=" OH  TYR A 404 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OE1 GLU B 387 "
            pdb=" OH  TYR B 404 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OD2 ASP B 491 "
            pdb=" OG  SER B 493 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD1 ASP A  52 "
            pdb=" OH  TYR A 405 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASP B  52 "
            pdb=" OH  TYR B 405 "
     model   vdw
     2.254 3.040
  ... (remaining 45880 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     18.650
  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:             0.000
  Load rotamer database and sin/cos tables:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
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      :  0.001   0.015   5842  Z= 0.088
  Angle     :  0.401   4.736   7902  Z= 0.207
  Chirality :  0.039   0.124    802
  Planarity :  0.003   0.032   1024
  Dihedral  :  7.771  54.148   2212
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  2.04 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.32), residues: 688
  helix:  0.69 (0.37), residues: 236
  sheet: -0.23 (0.51), residues: 110
  loop : -0.19 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 345 
 HIS   0.003   0.000   HIS B 395 
 PHE   0.006   0.001   PHE B 390 
 TYR   0.007   0.001   TYR B 369 
 ARG   0.001   0.000   ARG B 517 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 201
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.7276 (m110) cc_final: 0.5984 (m-40)
REVERT: A   50 LEU cc_start: 0.8162 (mt) cc_final: 0.7941 (mp)
REVERT: A   60 LYS cc_start: 0.8420 (mttm) cc_final: 0.7948 (mtpp)
REVERT: A   69 GLN cc_start: 0.8706 (mt0) cc_final: 0.8367 (tp40)
REVERT: A   92 LYS cc_start: 0.8121 (mttm) cc_final: 0.7884 (ptmt)
REVERT: A  281 ASP cc_start: 0.7399 (t0) cc_final: 0.7177 (t70)
REVERT: A  466 THR cc_start: 0.9333 (p) cc_final: 0.8979 (t)
REVERT: A  467 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8506 (mm-30)
REVERT: A  470 ARG cc_start: 0.8806 (mmt180) cc_final: 0.8210 (mmm-85)
REVERT: A  495 GLU cc_start: 0.8969 (tt0) cc_final: 0.8721 (tm-30)
REVERT: A  513 MET cc_start: 0.7586 (mtm) cc_final: 0.7373 (mtm)
REVERT: B   13 ASP cc_start: 0.8350 (t0) cc_final: 0.7746 (t0)
REVERT: B   74 GLN cc_start: 0.8789 (mt0) cc_final: 0.8574 (mt0)
REVERT: B   92 LYS cc_start: 0.9135 (tttt) cc_final: 0.8370 (ttpp)
REVERT: B   99 LYS cc_start: 0.9073 (tppt) cc_final: 0.8810 (tptp)
REVERT: B  103 LYS cc_start: 0.8860 (mttm) cc_final: 0.8570 (tmmt)
REVERT: B  270 LEU cc_start: 0.8563 (tp) cc_final: 0.8299 (tm)
REVERT: B  271 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7680 (mm-30)
REVERT: B  317 ARG cc_start: 0.8165 (mtp-110) cc_final: 0.7114 (tmt-80)
REVERT: B  325 GLU cc_start: 0.8328 (tt0) cc_final: 0.8099 (mm-30)
REVERT: B  416 MET cc_start: 0.8711 (mmt) cc_final: 0.8296 (mmp)
REVERT: B  500 GLN cc_start: 0.8638 (mt0) cc_final: 0.8287 (tp-100)
  outliers start: 3
  outliers final: 1
  residues processed: 203
  average time/residue: 1.1722
  time to fit residues: 248.3616
Evaluate side-chains
  111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A  40 HIS
A  83 GLN
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 GLN
A 489 GLN
B  35 ASN
B 304 GLN
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 440 GLN
B 472 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.102977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.089226 restraints weight = 12573.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 3.85
r_work: 0.3697 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5842  Z= 0.215
  Angle     :  0.658  11.821   7902  Z= 0.323
  Chirality :  0.045   0.161    802
  Planarity :  0.005   0.050   1024
  Dihedral  :  4.016  57.192    784
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.15 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.32), residues: 688
  helix:  0.55 (0.35), residues: 232
  sheet: -0.07 (0.53), residues: 108
  loop : -0.24 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  55 
 HIS   0.007   0.001   HIS B 395 
 PHE   0.016   0.002   PHE B 292 
 TYR   0.018   0.001   TYR A 404 
 ARG   0.007   0.001   ARG B 477 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.8258 (mt) cc_final: 0.8001 (mp)
REVERT: A   60 LYS cc_start: 0.8649 (mttm) cc_final: 0.8221 (mtpp)
REVERT: A   92 LYS cc_start: 0.8279 (mttm) cc_final: 0.7775 (ptmt)
REVERT: A   99 LYS cc_start: 0.8593 (tptp) cc_final: 0.8242 (mmmm)
REVERT: A  400 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8549 (tp-100)
REVERT: A  416 MET cc_start: 0.8628 (ppp) cc_final: 0.8220 (ppp)
REVERT: A  418 TYR cc_start: 0.7945 (p90) cc_final: 0.7671 (p90)
REVERT: A  419 LYS cc_start: 0.8567 (mttt) cc_final: 0.8138 (ptpp)
REVERT: A  466 THR cc_start: 0.9324 (p) cc_final: 0.8864 (t)
REVERT: A  467 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8403 (mm-30)
REVERT: A  470 ARG cc_start: 0.8884 (mmt180) cc_final: 0.8541 (mmm-85)
REVERT: B   13 ASP cc_start: 0.8475 (t0) cc_final: 0.8205 (t0)
REVERT: B   60 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8129 (mmmm)
REVERT: B   92 LYS cc_start: 0.8932 (tttt) cc_final: 0.8350 (ttpp)
REVERT: B   99 LYS cc_start: 0.8986 (tppt) cc_final: 0.8754 (tptp)
REVERT: B  270 LEU cc_start: 0.8614 (tp) cc_final: 0.8282 (tm)
REVERT: B  271 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7658 (mm-30)
REVERT: B  317 ARG cc_start: 0.7385 (mtp-110) cc_final: 0.7154 (tpt90)
REVERT: B  325 GLU cc_start: 0.8638 (tt0) cc_final: 0.8262 (mm-30)
REVERT: B  416 MET cc_start: 0.8591 (mmt) cc_final: 0.8119 (mmp)
REVERT: B  480 MET cc_start: 0.7607 (ptp) cc_final: 0.7386 (ptp)
  outliers start: 18
  outliers final: 6
  residues processed: 119
  average time/residue: 1.2656
  time to fit residues: 157.1754
Evaluate side-chains
  92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  342 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0570
   chunk 65 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** 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 = 0.4075 r_free = 0.4075 target = 0.102965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.087782 restraints weight = 12858.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 4.15
r_work: 0.3682 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5842  Z= 0.174
  Angle     :  0.617  10.420   7902  Z= 0.302
  Chirality :  0.047   0.396    802
  Planarity :  0.004   0.035   1024
  Dihedral  :  4.024  56.658    784
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 13.84 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.32), residues: 688
  helix:  0.49 (0.36), residues: 234
  sheet: -0.22 (0.49), residues: 118
  loop : -0.31 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  55 
 HIS   0.007   0.001   HIS B 341 
 PHE   0.014   0.001   PHE A 408 
 TYR   0.014   0.001   TYR A 404 
 ARG   0.005   0.000   ARG B 477 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ASN cc_start: 0.8416 (t0) cc_final: 0.8164 (t0)
REVERT: A   38 TRP cc_start: 0.7739 (OUTLIER) cc_final: 0.7320 (t-100)
REVERT: A   50 LEU cc_start: 0.8104 (mt) cc_final: 0.7872 (mp)
REVERT: A   60 LYS cc_start: 0.8694 (mttm) cc_final: 0.8258 (mtpp)
REVERT: A   92 LYS cc_start: 0.8133 (mttm) cc_final: 0.7596 (ttpp)
REVERT: A   99 LYS cc_start: 0.8383 (tptp) cc_final: 0.8144 (mmmm)
REVERT: A  400 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8616 (tp-100)
REVERT: A  464 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8310 (ptm-80)
REVERT: A  466 THR cc_start: 0.9368 (p) cc_final: 0.8913 (t)
REVERT: A  467 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8466 (mm-30)
REVERT: A  470 ARG cc_start: 0.8831 (mmt180) cc_final: 0.8432 (mmm-85)
REVERT: A  495 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8373 (tm-30)
REVERT: A  499 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8698 (mp)
REVERT: B   11 VAL cc_start: 0.8857 (t) cc_final: 0.8555 (p)
REVERT: B   13 ASP cc_start: 0.8418 (t0) cc_final: 0.8191 (t0)
REVERT: B   60 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8209 (mmmm)
REVERT: B   92 LYS cc_start: 0.9016 (tttt) cc_final: 0.8706 (ptmm)
REVERT: B   99 LYS cc_start: 0.9011 (tppt) cc_final: 0.8720 (tptp)
REVERT: B  270 LEU cc_start: 0.8582 (tp) cc_final: 0.8293 (tm)
REVERT: B  271 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7619 (mm-30)
REVERT: B  317 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7178 (tmt-80)
REVERT: B  325 GLU cc_start: 0.8704 (tt0) cc_final: 0.8309 (mm-30)
REVERT: B  416 MET cc_start: 0.8621 (mmt) cc_final: 0.8172 (mmp)
REVERT: B  433 TYR cc_start: 0.8132 (m-80) cc_final: 0.7769 (m-80)
  outliers start: 22
  outliers final: 7
  residues processed: 105
  average time/residue: 1.0923
  time to fit residues: 120.6135
Evaluate side-chains
  97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   95 LYS
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0170
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 500 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.100998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.085598 restraints weight = 13389.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 4.31
r_work: 0.3636 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5842  Z= 0.175
  Angle     :  0.578   8.956   7902  Z= 0.284
  Chirality :  0.045   0.246    802
  Planarity :  0.004   0.046   1024
  Dihedral  :  3.460  12.009    782
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.99 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.32), residues: 688
  helix:  0.48 (0.36), residues: 234
  sheet: -0.26 (0.49), residues: 118
  loop : -0.29 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  55 
 HIS   0.006   0.001   HIS B 341 
 PHE   0.016   0.001   PHE A 408 
 TYR   0.014   0.001   TYR A 382 
 ARG   0.002   0.000   ARG B 477 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.7147 (t-100)
REVERT: A   50 LEU cc_start: 0.8164 (mt) cc_final: 0.7910 (mp)
REVERT: A   60 LYS cc_start: 0.8669 (mttm) cc_final: 0.8311 (mtpt)
REVERT: A   64 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7277 (ttpp)
REVERT: A   67 MET cc_start: 0.8663 (mmt) cc_final: 0.8294 (mmt)
REVERT: A   92 LYS cc_start: 0.8024 (mttm) cc_final: 0.7615 (ptmt)
REVERT: A   99 LYS cc_start: 0.8607 (tptp) cc_final: 0.8387 (mmmm)
REVERT: A  400 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8643 (tp-100)
REVERT: A  464 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8377 (ptm-80)
REVERT: A  466 THR cc_start: 0.9388 (p) cc_final: 0.8931 (t)
REVERT: A  467 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8566 (mm-30)
REVERT: A  470 ARG cc_start: 0.8849 (mmt180) cc_final: 0.8572 (mmm160)
REVERT: A  480 MET cc_start: 0.7495 (ptp) cc_final: 0.7240 (ptt)
REVERT: A  495 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8354 (tm-30)
REVERT: A  499 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8650 (mp)
REVERT: B   11 VAL cc_start: 0.8825 (t) cc_final: 0.8534 (p)
REVERT: B   60 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8193 (mmmm)
REVERT: B   92 LYS cc_start: 0.9038 (tttt) cc_final: 0.8535 (ptmm)
REVERT: B   99 LYS cc_start: 0.9066 (tppt) cc_final: 0.8760 (tptp)
REVERT: B  270 LEU cc_start: 0.8553 (tp) cc_final: 0.8332 (tm)
REVERT: B  271 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7813 (mm-30)
REVERT: B  273 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6889 (mpt-90)
REVERT: B  317 ARG cc_start: 0.7484 (mtp-110) cc_final: 0.7024 (tpt90)
REVERT: B  325 GLU cc_start: 0.8674 (tt0) cc_final: 0.8287 (mm-30)
REVERT: B  396 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: B  406 MET cc_start: 0.7459 (mmm) cc_final: 0.7202 (mmm)
REVERT: B  416 MET cc_start: 0.8715 (mmt) cc_final: 0.8295 (mmp)
REVERT: B  477 ARG cc_start: 0.8004 (mtm110) cc_final: 0.7337 (ttp-170)
  outliers start: 21
  outliers final: 7
  residues processed: 103
  average time/residue: 1.1769
  time to fit residues: 127.5052
Evaluate side-chains
  93 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  400 GLN
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   15 PHE
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    0.1980
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 HIS
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.099943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.084693 restraints weight = 13039.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 4.22
r_work: 0.3624 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5842  Z= 0.185
  Angle     :  0.587   8.882   7902  Z= 0.286
  Chirality :  0.045   0.201    802
  Planarity :  0.004   0.047   1024
  Dihedral  :  3.519  15.130    782
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.72 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.32), residues: 688
  helix:  0.46 (0.36), residues: 234
  sheet: -0.46 (0.50), residues: 118
  loop : -0.24 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  38 
 HIS   0.004   0.001   HIS B 341 
 PHE   0.020   0.001   PHE B  15 
 TYR   0.026   0.001   TYR A 422 
 ARG   0.010   0.000   ARG B  22 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7766 (OUTLIER) cc_final: 0.7157 (t-100)
REVERT: A   50 LEU cc_start: 0.8193 (mt) cc_final: 0.7930 (mp)
REVERT: A   60 LYS cc_start: 0.8594 (mttm) cc_final: 0.8192 (mmmm)
REVERT: A   64 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7299 (ttpp)
REVERT: A   92 LYS cc_start: 0.8019 (mttm) cc_final: 0.7602 (ttpp)
REVERT: A  464 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8303 (ptm-80)
REVERT: A  466 THR cc_start: 0.9404 (p) cc_final: 0.9039 (t)
REVERT: A  467 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8584 (mm-30)
REVERT: A  495 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8368 (tm-30)
REVERT: A  499 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8619 (mp)
REVERT: B   11 VAL cc_start: 0.8790 (t) cc_final: 0.8462 (p)
REVERT: B   60 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8175 (mmmm)
REVERT: B   92 LYS cc_start: 0.9038 (tttt) cc_final: 0.8680 (ptmm)
REVERT: B   99 LYS cc_start: 0.9060 (tppt) cc_final: 0.8769 (tptp)
REVERT: B  270 LEU cc_start: 0.8577 (tp) cc_final: 0.8258 (tt)
REVERT: B  271 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7840 (mm-30)
REVERT: B  273 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6910 (mpt-90)
REVERT: B  317 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.7124 (tpt90)
REVERT: B  325 GLU cc_start: 0.8672 (tt0) cc_final: 0.8270 (mm-30)
REVERT: B  396 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8196 (mm-30)
REVERT: B  406 MET cc_start: 0.7337 (mmm) cc_final: 0.7012 (mmm)
REVERT: B  416 MET cc_start: 0.8746 (mmt) cc_final: 0.8269 (mmp)
REVERT: B  477 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7271 (ttt-90)
  outliers start: 14
  outliers final: 6
  residues processed: 94
  average time/residue: 1.1233
  time to fit residues: 111.1307
Evaluate side-chains
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.094000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.080041 restraints weight = 13496.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 3.99
r_work: 0.3538 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5842  Z= 0.294
  Angle     :  0.668   9.208   7902  Z= 0.332
  Chirality :  0.047   0.203    802
  Planarity :  0.004   0.051   1024
  Dihedral  :  3.784  18.858    782
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.41 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.32), residues: 688
  helix:  0.44 (0.36), residues: 228
  sheet: -0.73 (0.48), residues: 120
  loop : -0.22 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  55 
 HIS   0.006   0.002   HIS B 341 
 PHE   0.020   0.002   PHE B 516 
 TYR   0.017   0.002   TYR B 404 
 ARG   0.007   0.001   ARG B  22 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7728 (OUTLIER) cc_final: 0.7183 (t-100)
REVERT: A   50 LEU cc_start: 0.8305 (mt) cc_final: 0.7977 (mp)
REVERT: A   60 LYS cc_start: 0.8617 (mttm) cc_final: 0.8273 (mtpt)
REVERT: A   64 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7165 (ttpp)
REVERT: A   92 LYS cc_start: 0.8072 (mttm) cc_final: 0.7811 (ttpp)
REVERT: A   99 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8647 (mmtm)
REVERT: A  325 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8228 (mp0)
REVERT: A  353 VAL cc_start: 0.8640 (t) cc_final: 0.8326 (t)
REVERT: A  464 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8412 (ptm-80)
REVERT: A  466 THR cc_start: 0.9415 (p) cc_final: 0.9100 (t)
REVERT: A  467 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8772 (mm-30)
REVERT: A  495 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8302 (tm-30)
REVERT: A  499 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8667 (mp)
REVERT: B   60 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8151 (mmmm)
REVERT: B   92 LYS cc_start: 0.9152 (tttt) cc_final: 0.8822 (ptmm)
REVERT: B   99 LYS cc_start: 0.9089 (tppt) cc_final: 0.8789 (tptp)
REVERT: B  271 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7849 (mm-30)
REVERT: B  273 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7011 (mpt-90)
REVERT: B  281 ASP cc_start: 0.7884 (t70) cc_final: 0.7595 (t70)
REVERT: B  317 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7271 (tmt-80)
REVERT: B  325 GLU cc_start: 0.8745 (tt0) cc_final: 0.8349 (mp0)
REVERT: B  396 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8204 (mm-30)
REVERT: B  406 MET cc_start: 0.7669 (mmm) cc_final: 0.7394 (mmm)
REVERT: B  416 MET cc_start: 0.8781 (mmt) cc_final: 0.8327 (mmp)
REVERT: B  477 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7342 (ttp-170)
  outliers start: 21
  outliers final: 10
  residues processed: 98
  average time/residue: 1.1184
  time to fit residues: 115.2149
Evaluate side-chains
  93 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   74 GLN
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  317 ARG
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** 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 = 0.3966 r_free = 0.3966 target = 0.096117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.081993 restraints weight = 13396.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 4.02
r_work: 0.3582 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5842  Z= 0.188
  Angle     :  0.621  11.255   7902  Z= 0.309
  Chirality :  0.045   0.180    802
  Planarity :  0.004   0.051   1024
  Dihedral  :  3.717  19.523    782
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.98 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.32), residues: 688
  helix:  0.38 (0.35), residues: 234
  sheet: -0.19 (0.51), residues: 102
  loop : -0.35 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  55 
 HIS   0.005   0.001   HIS B 341 
 PHE   0.014   0.001   PHE A 408 
 TYR   0.012   0.001   TYR B 404 
 ARG   0.006   0.001   ARG B 317 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7734 (OUTLIER) cc_final: 0.7356 (t-100)
REVERT: A   50 LEU cc_start: 0.8273 (mt) cc_final: 0.8027 (mp)
REVERT: A   60 LYS cc_start: 0.8572 (mttm) cc_final: 0.8263 (mtpt)
REVERT: A   92 LYS cc_start: 0.8057 (mttm) cc_final: 0.7796 (ptmt)
REVERT: A  318 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6690 (m-10)
REVERT: A  464 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8407 (ptm-80)
REVERT: A  466 THR cc_start: 0.9460 (p) cc_final: 0.9163 (t)
REVERT: A  467 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8720 (mm-30)
REVERT: A  495 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8374 (tm-30)
REVERT: A  499 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8654 (mp)
REVERT: B   92 LYS cc_start: 0.9130 (tttt) cc_final: 0.8806 (ptmm)
REVERT: B   99 LYS cc_start: 0.9080 (tppt) cc_final: 0.8792 (tptp)
REVERT: B  271 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7846 (mm-30)
REVERT: B  273 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6935 (mpt-90)
REVERT: B  317 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7296 (tmt-80)
REVERT: B  325 GLU cc_start: 0.8762 (tt0) cc_final: 0.8411 (mp0)
REVERT: B  396 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8210 (mm-30)
REVERT: B  406 MET cc_start: 0.7649 (mmm) cc_final: 0.7356 (mmm)
REVERT: B  416 MET cc_start: 0.8789 (mmt) cc_final: 0.8347 (mmp)
REVERT: B  477 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7303 (ttm-80)
  outliers start: 16
  outliers final: 6
  residues processed: 88
  average time/residue: 1.1788
  time to fit residues: 108.8799
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   74 GLN
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  317 ARG
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** 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 = 0.3971 r_free = 0.3971 target = 0.096431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.081786 restraints weight = 13333.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 4.08
r_work: 0.3573 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5842  Z= 0.184
  Angle     :  0.614   9.939   7902  Z= 0.300
  Chirality :  0.045   0.173    802
  Planarity :  0.004   0.052   1024
  Dihedral  :  3.732  21.636    782
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.30 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.32), residues: 688
  helix:  0.37 (0.35), residues: 234
  sheet: -0.25 (0.51), residues: 102
  loop : -0.35 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  55 
 HIS   0.005   0.001   HIS B 395 
 PHE   0.012   0.001   PHE A 408 
 TYR   0.014   0.001   TYR B 404 
 ARG   0.005   0.000   ARG B 317 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.6866 (m-80) cc_final: 0.6635 (m-80)
REVERT: A   38 TRP cc_start: 0.7686 (OUTLIER) cc_final: 0.7189 (t-100)
REVERT: A   50 LEU cc_start: 0.8375 (mt) cc_final: 0.8089 (mt)
REVERT: A   55 TRP cc_start: 0.8021 (m100) cc_final: 0.7741 (m100)
REVERT: A   60 LYS cc_start: 0.8533 (mttm) cc_final: 0.8186 (mtpp)
REVERT: A   92 LYS cc_start: 0.8105 (mttm) cc_final: 0.7770 (ptmt)
REVERT: A  325 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8228 (mp0)
REVERT: A  401 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8250 (tm)
REVERT: A  464 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8453 (ptm-80)
REVERT: A  466 THR cc_start: 0.9467 (p) cc_final: 0.9137 (t)
REVERT: A  467 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8735 (mm-30)
REVERT: A  495 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8284 (tm-30)
REVERT: A  499 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8711 (mp)
REVERT: B   92 LYS cc_start: 0.9178 (tttt) cc_final: 0.8889 (ptmm)
REVERT: B   99 LYS cc_start: 0.9094 (tppt) cc_final: 0.8804 (tptp)
REVERT: B  271 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7923 (mm-30)
REVERT: B  273 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6932 (mpt-90)
REVERT: B  281 ASP cc_start: 0.7864 (t70) cc_final: 0.7543 (t70)
REVERT: B  317 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7322 (tmt-80)
REVERT: B  325 GLU cc_start: 0.8798 (tt0) cc_final: 0.8439 (mp0)
REVERT: B  396 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8257 (mm-30)
REVERT: B  406 MET cc_start: 0.7712 (mmm) cc_final: 0.7478 (mmm)
REVERT: B  416 MET cc_start: 0.8776 (mmt) cc_final: 0.8354 (mmp)
  outliers start: 16
  outliers final: 6
  residues processed: 90
  average time/residue: 1.2026
  time to fit residues: 113.6178
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  317 ARG
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** 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 = 0.3940 r_free = 0.3940 target = 0.094679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.080563 restraints weight = 13406.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 4.03
r_work: 0.3544 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.5115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5842  Z= 0.222
  Angle     :  0.643   9.907   7902  Z= 0.313
  Chirality :  0.047   0.241    802
  Planarity :  0.004   0.052   1024
  Dihedral  :  3.813  19.466    782
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.98 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.32), residues: 688
  helix:  0.34 (0.35), residues: 234
  sheet: -0.54 (0.54), residues: 100
  loop : -0.28 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  55 
 HIS   0.005   0.001   HIS B 341 
 PHE   0.013   0.001   PHE B 516 
 TYR   0.013   0.001   TYR B 404 
 ARG   0.005   0.000   ARG B 317 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.8333 (mt) cc_final: 0.7964 (mt)
REVERT: A   55 TRP cc_start: 0.8156 (m100) cc_final: 0.7943 (m100)
REVERT: A   92 LYS cc_start: 0.8338 (mttm) cc_final: 0.8012 (ptmt)
REVERT: A   99 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8695 (mmtm)
REVERT: A  325 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8174 (mp0)
REVERT: A  401 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8205 (tm)
REVERT: A  433 TYR cc_start: 0.7930 (m-80) cc_final: 0.7523 (m-80)
REVERT: A  464 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8464 (ptm-80)
REVERT: A  466 THR cc_start: 0.9477 (p) cc_final: 0.9145 (t)
REVERT: A  467 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8815 (mm-30)
REVERT: A  495 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8380 (tm-30)
REVERT: A  499 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8714 (mp)
REVERT: B   92 LYS cc_start: 0.9231 (tttt) cc_final: 0.8952 (ptmm)
REVERT: B   99 LYS cc_start: 0.9106 (tppt) cc_final: 0.8764 (tptp)
REVERT: B  271 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7906 (mm-30)
REVERT: B  273 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7033 (mpt-90)
REVERT: B  317 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7347 (tmt-80)
REVERT: B  325 GLU cc_start: 0.8849 (tt0) cc_final: 0.8421 (mp0)
REVERT: B  396 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8241 (mm-30)
REVERT: B  406 MET cc_start: 0.7675 (mmm) cc_final: 0.7359 (mmm)
REVERT: B  410 ILE cc_start: 0.7734 (mm) cc_final: 0.7408 (tp)
REVERT: B  416 MET cc_start: 0.8773 (mmt) cc_final: 0.8403 (mmp)
  outliers start: 17
  outliers final: 5
  residues processed: 86
  average time/residue: 1.1942
  time to fit residues: 107.7832
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  317 ARG
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0970
   chunk 51 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.095956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.081534 restraints weight = 13588.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 4.07
r_work: 0.3572 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.5283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5842  Z= 0.199
  Angle     :  0.676  11.118   7902  Z= 0.326
  Chirality :  0.047   0.264    802
  Planarity :  0.004   0.052   1024
  Dihedral  :  3.904  20.146    782
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.61 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.32), residues: 688
  helix:  0.35 (0.35), residues: 234
  sheet: -0.18 (0.55), residues: 90
  loop : -0.35 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  38 
 HIS   0.004   0.001   HIS B 395 
 PHE   0.017   0.001   PHE B 516 
 TYR   0.012   0.001   TYR A 370 
 ARG   0.005   0.000   ARG B 317 

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7517 (OUTLIER) cc_final: 0.6876 (m-90)
REVERT: A   50 LEU cc_start: 0.8356 (mt) cc_final: 0.7977 (mt)
REVERT: A   55 TRP cc_start: 0.8157 (m100) cc_final: 0.7955 (m100)
REVERT: A   92 LYS cc_start: 0.8301 (mttm) cc_final: 0.7859 (ptmt)
REVERT: A  318 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6437 (m-10)
REVERT: A  325 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8215 (mp0)
REVERT: A  401 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8181 (tm)
REVERT: A  419 LYS cc_start: 0.8552 (mttt) cc_final: 0.8127 (mtmm)
REVERT: A  464 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8425 (ptm-80)
REVERT: A  495 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8374 (tm-30)
REVERT: A  499 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8718 (mp)
REVERT: B   60 LYS cc_start: 0.8546 (mmmm) cc_final: 0.8029 (mmtp)
REVERT: B   92 LYS cc_start: 0.9234 (tttt) cc_final: 0.8892 (ptmm)
REVERT: B   99 LYS cc_start: 0.9113 (tppt) cc_final: 0.8781 (tptp)
REVERT: B  271 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7895 (mm-30)
REVERT: B  273 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6923 (mpt-90)
REVERT: B  325 GLU cc_start: 0.8836 (tt0) cc_final: 0.8430 (mp0)
REVERT: B  396 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8117 (mm-30)
REVERT: B  406 MET cc_start: 0.7720 (mmm) cc_final: 0.7414 (mmm)
REVERT: B  410 ILE cc_start: 0.7568 (mm) cc_final: 0.7237 (tp)
REVERT: B  416 MET cc_start: 0.8768 (mmt) cc_final: 0.8400 (mmp)
REVERT: B  477 ARG cc_start: 0.7564 (mtm110) cc_final: 0.6921 (ttt-90)
  outliers start: 13
  outliers final: 5
  residues processed: 85
  average time/residue: 1.1058
  time to fit residues: 98.9334
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0870
   chunk 30 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 ASN
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.097210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.082530 restraints weight = 13667.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 4.17
r_work: 0.3596 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.5327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   5842  Z= 0.184
  Angle     :  0.682  11.260   7902  Z= 0.326
  Chirality :  0.047   0.249    802
  Planarity :  0.004   0.052   1024
  Dihedral  :  3.860  20.300    782
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.87 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.32), residues: 688
  helix:  0.41 (0.35), residues: 234
  sheet: -0.17 (0.55), residues: 90
  loop : -0.33 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  38 
 HIS   0.006   0.001   HIS B 341 
 PHE   0.020   0.001   PHE B 516 
 TYR   0.022   0.001   TYR A 382 
 ARG   0.004   0.000   ARG B 517 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4169.09 seconds
wall clock time: 74 minutes 16.36 seconds (4456.36 seconds total)