Starting phenix.real_space_refine
on Fri Aug 22 16:18:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzv_41770/08_2025/8tzv_41770.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzv_41770/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2025/8tzv_41770.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2025/8tzv_41770.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2025/8tzv_41770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2025/8tzv_41770.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.90, per 1000 atoms: 0.33
  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: 0.49
  Conformation dependent library (CDL) restraints added in 217.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 0.22
  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: 0.86

  Time building geometry restraints manager: 0.72 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: 0.01
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:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.500
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:6.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.400
-------------------------------------------------------------------------------
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      :  0.002   0.037   5850  Z= 0.079
  Angle     :  1.218  49.160   7914  Z= 0.295
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG B 517 
 TYR   0.007   0.001   TYR B 369 
 PHE   0.006   0.001   PHE B 390 
 TRP   0.005   0.001   TRP A 345 
 HIS   0.003   0.000   HIS B 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00136 ( 5842)
  covalent geometry    : angle       0.40051 ( 7902)
  hydrogen bonds       : bond        0.17600 (  221)
  hydrogen bonds       : angle       7.07185 (  600)
  metal coordination   : bond        0.02023 (    8)
  metal coordination   : angle      29.55387 (   12)

*********************** 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  : 0.225 
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: 0.7945 (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: 0.8980 (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: 0.7374 (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: 0.8548 (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: 0.8298 (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: 0.7130 (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: 0.8293 (mmp)
  outliers start: 3
  outliers final: 1
  residues processed: 203
  average time/residue: 0.5821
  time to fit residues: 123.2050
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  : 0.240 
-------------------------------------------------------------------------------
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 49 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0030
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.2994

-------------------------------------------------------------------------------
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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 GLN
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 GLN
A 489 GLN
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.100664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.086258 restraints weight = 12939.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 4.08
r_work: 0.3641 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5850  Z= 0.179
  Angle     :  1.078  43.128   7914  Z= 0.370
  Chirality :  0.046   0.150    802
  Planarity :  0.005   0.043   1024
  Dihedral  :  4.199  59.075    784
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.15 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.32), residues: 688
  helix:  0.49 (0.35), residues: 232
  sheet: -0.06 (0.52), residues: 106
  loop : -0.30 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 477 
 TYR   0.018   0.002   TYR A 404 
 PHE   0.020   0.002   PHE B 292 
 TRP   0.008   0.001   TRP B  55 
 HIS   0.007   0.001   HIS B 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5842)
  covalent geometry    : angle       0.68581 ( 7902)
  hydrogen bonds       : bond        0.04004 (  221)
  hydrogen bonds       : angle       4.99664 (  600)
  metal coordination   : bond        0.01178 (    8)
  metal coordination   : angle      21.38275 (   12)

*********************** 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
  124 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.284 
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: 0.8224 (mt) cc_final: 0.7919 (mp)
REVERT: A   60 LYS cc_start: 0.8657 (mttm) cc_final: 0.8215 (mtpt)
REVERT: A   92 LYS cc_start: 0.8293 (mttm) cc_final: 0.7887 (ttpp)
REVERT: A   99 LYS cc_start: 0.8629 (tptp) cc_final: 0.8261 (mmmm)
REVERT: A  400 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8592 (tp-100)
REVERT: A  418 TYR cc_start: 0.7986 (p90) cc_final: 0.7695 (p90)
REVERT: A  419 LYS cc_start: 0.8567 (mttt) cc_final: 0.8138 (ptpp)
REVERT: A  466 THR cc_start: 0.9375 (p) cc_final: 0.9166 (t)
REVERT: A  467 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8585 (mm-30)
REVERT: A  470 ARG cc_start: 0.8862 (mmt180) cc_final: 0.8494 (mmm-85)
REVERT: A  513 MET cc_start: 0.7381 (mtm) cc_final: 0.7113 (mtm)
REVERT: B   13 ASP cc_start: 0.8477 (t0) cc_final: 0.8153 (t0)
REVERT: B   60 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8161 (mmmm)
REVERT: B   92 LYS cc_start: 0.8952 (tttt) cc_final: 0.8392 (ttpp)
REVERT: B   99 LYS cc_start: 0.9008 (tppt) cc_final: 0.8795 (tptp)
REVERT: B  103 LYS cc_start: 0.8972 (mttm) cc_final: 0.8651 (tptp)
REVERT: B  270 LEU cc_start: 0.8594 (tp) cc_final: 0.8285 (tm)
REVERT: B  271 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7845 (mm-30)
REVERT: B  325 GLU cc_start: 0.8623 (tt0) cc_final: 0.8230 (mm-30)
REVERT: B  416 MET cc_start: 0.8652 (mmt) cc_final: 0.8195 (mmp)
REVERT: B  477 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7072 (ttp-110)
REVERT: B  480 MET cc_start: 0.7435 (ptp) cc_final: 0.7194 (ptp)
  outliers start: 19
  outliers final: 7
  residues processed: 115
  average time/residue: 0.6459
  time to fit residues: 77.3406
Evaluate side-chains
  91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue  368 LEU
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  460 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0170
   chunk 59 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.1422

-------------------------------------------------------------------------------
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  35 ASN ** 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 = 0.4003 r_free = 0.4003 target = 0.098375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.083360 restraints weight = 13170.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 4.20
r_work: 0.3599 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5850  Z= 0.154
  Angle     :  1.000  42.619   7914  Z= 0.343
  Chirality :  0.047   0.387    802
  Planarity :  0.004   0.037   1024
  Dihedral  :  4.045  50.378    784
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 13.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.32), residues: 688
  helix:  0.32 (0.35), residues: 236
  sheet: -0.42 (0.49), residues: 118
  loop : -0.30 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 517 
 TYR   0.015   0.001   TYR A 404 
 PHE   0.015   0.002   PHE B  15 
 TRP   0.009   0.002   TRP B  38 
 HIS   0.007   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5842)
  covalent geometry    : angle       0.62576 ( 7902)
  hydrogen bonds       : bond        0.03697 (  221)
  hydrogen bonds       : angle       4.87280 (  600)
  metal coordination   : bond        0.00913 (    8)
  metal coordination   : angle      20.05355 (   12)

*********************** 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
  117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.236 
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   50 LEU cc_start: 0.8134 (mt) cc_final: 0.7815 (mp)
REVERT: A   60 LYS cc_start: 0.8714 (mttm) cc_final: 0.8368 (mtpp)
REVERT: A   64 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6832 (tptm)
REVERT: A   92 LYS cc_start: 0.8014 (mttm) cc_final: 0.7748 (ttpp)
REVERT: A   99 LYS cc_start: 0.8430 (tptp) cc_final: 0.8188 (mmmm)
REVERT: A  400 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (tp-100)
REVERT: A  416 MET cc_start: 0.8810 (ppp) cc_final: 0.8545 (ppp)
REVERT: A  464 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8423 (ptm-80)
REVERT: A  466 THR cc_start: 0.9397 (p) cc_final: 0.9136 (t)
REVERT: A  467 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8725 (mm-30)
REVERT: A  495 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8421 (tm-30)
REVERT: A  499 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8708 (mp)
REVERT: B   13 ASP cc_start: 0.8413 (t0) cc_final: 0.8203 (t0)
REVERT: B   60 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8223 (mmmm)
REVERT: B   92 LYS cc_start: 0.9104 (tttt) cc_final: 0.8791 (ptmm)
REVERT: B   99 LYS cc_start: 0.9011 (tppt) cc_final: 0.8742 (tptp)
REVERT: B  103 LYS cc_start: 0.8910 (mttm) cc_final: 0.8685 (tptp)
REVERT: B  270 LEU cc_start: 0.8436 (tp) cc_final: 0.8131 (tt)
REVERT: B  271 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7895 (mm-30)
REVERT: B  273 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6960 (mpt-90)
REVERT: B  325 GLU cc_start: 0.8690 (tt0) cc_final: 0.8273 (mm-30)
REVERT: B  416 MET cc_start: 0.8770 (mmt) cc_final: 0.8343 (mmp)
REVERT: B  477 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7264 (ttt-90)
REVERT: B  480 MET cc_start: 0.7428 (ptp) cc_final: 0.7201 (ptp)
  outliers start: 25
  outliers final: 10
  residues processed: 106
  average time/residue: 0.5699
  time to fit residues: 63.3300
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  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   64 LYS
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   15 PHE
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  273 ARG
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  518 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    1.3188

-------------------------------------------------------------------------------
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  35 ASN
B 303 HIS
B 331 ASN
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.096262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.081259 restraints weight = 13382.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 4.20
r_work: 0.3560 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5850  Z= 0.167
  Angle     :  0.972  41.702   7914  Z= 0.337
  Chirality :  0.046   0.224    802
  Planarity :  0.004   0.041   1024
  Dihedral  :  3.652  14.297    782
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 13.99 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.32), residues: 688
  helix:  0.34 (0.35), residues: 234
  sheet: -0.53 (0.49), residues: 118
  loop : -0.27 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  22 
 TYR   0.020   0.002   TYR A 422 
 PHE   0.020   0.002   PHE B  15 
 TRP   0.012   0.002   TRP B  38 
 HIS   0.006   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5842)
  covalent geometry    : angle       0.62344 ( 7902)
  hydrogen bonds       : bond        0.03537 (  221)
  hydrogen bonds       : angle       4.93074 (  600)
  metal coordination   : bond        0.01034 (    8)
  metal coordination   : angle      19.14802 (   12)

*********************** 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
  113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.241 
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: 0.7677 (OUTLIER) cc_final: 0.7288 (t-100)
REVERT: A   50 LEU cc_start: 0.8205 (mt) cc_final: 0.7877 (mp)
REVERT: A   60 LYS cc_start: 0.8734 (mttm) cc_final: 0.8372 (mtpt)
REVERT: A   67 MET cc_start: 0.8787 (mmt) cc_final: 0.8351 (mmt)
REVERT: A   99 LYS cc_start: 0.8549 (tptp) cc_final: 0.8317 (mmmm)
REVERT: A  419 LYS cc_start: 0.8513 (mttt) cc_final: 0.8123 (mtmm)
REVERT: A  466 THR cc_start: 0.9438 (p) cc_final: 0.9180 (t)
REVERT: A  467 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8738 (mm-30)
REVERT: A  495 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8389 (tm-30)
REVERT: A  499 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8710 (mp)
REVERT: B   13 ASP cc_start: 0.8289 (t0) cc_final: 0.8049 (t0)
REVERT: B   60 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8233 (mmmm)
REVERT: B   92 LYS cc_start: 0.9079 (tttt) cc_final: 0.8618 (ptmm)
REVERT: B   99 LYS cc_start: 0.9041 (tppt) cc_final: 0.8755 (tptp)
REVERT: B  103 LYS cc_start: 0.9054 (mttm) cc_final: 0.8745 (tptp)
REVERT: B  271 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7809 (mm-30)
REVERT: B  273 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7007 (mpt-90)
REVERT: B  325 GLU cc_start: 0.8744 (tt0) cc_final: 0.8359 (mp0)
REVERT: B  392 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7228 (mtt-85)
REVERT: B  416 MET cc_start: 0.8808 (mmt) cc_final: 0.8338 (mmp)
REVERT: B  477 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7281 (ttp-170)
REVERT: B  480 MET cc_start: 0.7513 (ptp) cc_final: 0.7246 (ptp)
  outliers start: 26
  outliers final: 11
  residues processed: 102
  average time/residue: 0.5738
  time to fit residues: 61.2741
Evaluate side-chains
  92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   38 TRP
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  401 LEU
Chi-restraints excluded: chain A residue  493 SER
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  316 THR
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 60 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.093929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.078963 restraints weight = 13774.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 4.20
r_work: 0.3517 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.4765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5850  Z= 0.184
  Angle     :  0.888  35.743   7914  Z= 0.339
  Chirality :  0.047   0.297    802
  Planarity :  0.004   0.043   1024
  Dihedral  :  3.814  14.723    782
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.32), residues: 688
  helix:  0.42 (0.36), residues: 228
  sheet: -0.90 (0.46), residues: 120
  loop : -0.26 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 464 
 TYR   0.015   0.001   TYR B 404 
 PHE   0.016   0.002   PHE A 408 
 TRP   0.013   0.002   TRP A  55 
 HIS   0.006   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 5842)
  covalent geometry    : angle       0.65209 ( 7902)
  hydrogen bonds       : bond        0.03634 (  221)
  hydrogen bonds       : angle       5.08242 (  600)
  metal coordination   : bond        0.01375 (    8)
  metal coordination   : angle      15.48986 (   12)

*********************** 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
  110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.244 
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: 0.7792 (OUTLIER) cc_final: 0.7138 (t-100)
REVERT: A   50 LEU cc_start: 0.8287 (mt) cc_final: 0.7971 (mp)
REVERT: A   60 LYS cc_start: 0.8693 (mttm) cc_final: 0.8344 (mtpt)
REVERT: A   99 LYS cc_start: 0.8649 (tptp) cc_final: 0.8402 (tptp)
REVERT: A  353 VAL cc_start: 0.8645 (t) cc_final: 0.8340 (t)
REVERT: A  419 LYS cc_start: 0.8516 (mttt) cc_final: 0.8102 (mtmm)
REVERT: A  466 THR cc_start: 0.9377 (p) cc_final: 0.9172 (t)
REVERT: A  467 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8893 (mm-30)
REVERT: A  480 MET cc_start: 0.7495 (ppp) cc_final: 0.6751 (pp-130)
REVERT: A  495 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8441 (tm-30)
REVERT: A  499 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8718 (mp)
REVERT: B   13 ASP cc_start: 0.8404 (t0) cc_final: 0.8133 (t0)
REVERT: B   60 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8108 (mmmm)
REVERT: B   92 LYS cc_start: 0.9100 (tttt) cc_final: 0.8730 (ptmm)
REVERT: B   97 MET cc_start: 0.8734 (tmm) cc_final: 0.8523 (tmm)
REVERT: B   99 LYS cc_start: 0.9056 (tppt) cc_final: 0.8794 (tptp)
REVERT: B  103 LYS cc_start: 0.9064 (mttm) cc_final: 0.8801 (tptp)
REVERT: B  271 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7798 (mm-30)
REVERT: B  273 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7045 (mpt-90)
REVERT: B  325 GLU cc_start: 0.8773 (tt0) cc_final: 0.8330 (mp0)
REVERT: B  392 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7283 (mtt-85)
REVERT: B  406 MET cc_start: 0.7951 (mmm) cc_final: 0.7640 (mmm)
REVERT: B  416 MET cc_start: 0.8836 (mmt) cc_final: 0.8382 (mmp)
  outliers start: 25
  outliers final: 11
  residues processed: 101
  average time/residue: 0.5731
  time to fit residues: 60.6197
Evaluate side-chains
  90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   38 TRP
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  493 SER
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  290 GLN
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  388 ILE
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 5 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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
B 400 GLN
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.093236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.078757 restraints weight = 13682.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 4.03
r_work: 0.3521 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.5043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5850  Z= 0.181
  Angle     :  0.715  17.922   7914  Z= 0.328
  Chirality :  0.049   0.307    802
  Planarity :  0.004   0.046   1024
  Dihedral  :  3.903  18.821    782
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.32), residues: 688
  helix:  0.47 (0.36), residues: 228
  sheet: -1.02 (0.46), residues: 120
  loop : -0.36 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 464 
 TYR   0.014   0.001   TYR B 404 
 PHE   0.016   0.002   PHE A 408 
 TRP   0.013   0.002   TRP B  38 
 HIS   0.006   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 5842)
  covalent geometry    : angle       0.65654 ( 7902)
  hydrogen bonds       : bond        0.03601 (  221)
  hydrogen bonds       : angle       5.09990 (  600)
  metal coordination   : bond        0.00981 (    8)
  metal coordination   : angle       7.31380 (   12)

*********************** 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
  98 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7240 (t-100)
REVERT: A   50 LEU cc_start: 0.8345 (mt) cc_final: 0.7978 (mt)
REVERT: A   55 TRP cc_start: 0.8186 (m100) cc_final: 0.7973 (m100)
REVERT: A   60 LYS cc_start: 0.8669 (mttm) cc_final: 0.8300 (mtpp)
REVERT: A   99 LYS cc_start: 0.8789 (tptp) cc_final: 0.8541 (tptp)
REVERT: A  419 LYS cc_start: 0.8530 (mttt) cc_final: 0.8159 (mtmm)
REVERT: A  433 TYR cc_start: 0.7968 (m-80) cc_final: 0.7489 (m-80)
REVERT: A  466 THR cc_start: 0.9428 (p) cc_final: 0.9216 (t)
REVERT: A  467 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8857 (mm-30)
REVERT: A  480 MET cc_start: 0.7453 (ppp) cc_final: 0.7170 (pp-130)
REVERT: A  495 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8410 (tm-30)
REVERT: A  499 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8740 (mp)
REVERT: B   13 ASP cc_start: 0.8453 (t0) cc_final: 0.8215 (t0)
REVERT: B   60 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8134 (mmmm)
REVERT: B   92 LYS cc_start: 0.9176 (tttt) cc_final: 0.8852 (ptmm)
REVERT: B   99 LYS cc_start: 0.9150 (tppt) cc_final: 0.8807 (tptp)
REVERT: B  103 LYS cc_start: 0.9082 (mttm) cc_final: 0.8826 (tptp)
REVERT: B  271 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7863 (mm-30)
REVERT: B  273 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6952 (mpt-90)
REVERT: B  325 GLU cc_start: 0.8872 (tt0) cc_final: 0.8564 (mt-10)
REVERT: B  406 MET cc_start: 0.7641 (mmm) cc_final: 0.7331 (mmm)
REVERT: B  416 MET cc_start: 0.8841 (mmt) cc_final: 0.8411 (mmp)
  outliers start: 23
  outliers final: 11
  residues processed: 86
  average time/residue: 0.5448
  time to fit residues: 49.2888
Evaluate side-chains
  88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  518 ASN
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  316 THR
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 23 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0470
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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**
** 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 = 0.3946 r_free = 0.3946 target = 0.094935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.080540 restraints weight = 13789.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 4.09
r_work: 0.3552 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5850  Z= 0.120
  Angle     :  0.676  14.388   7914  Z= 0.315
  Chirality :  0.047   0.292    802
  Planarity :  0.004   0.045   1024
  Dihedral  :  3.845  21.150    782
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.32), residues: 688
  helix:  0.57 (0.36), residues: 226
  sheet: -1.07 (0.45), residues: 128
  loop : -0.26 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 464 
 TYR   0.024   0.001   TYR A 422 
 PHE   0.019   0.001   PHE B 516 
 TRP   0.016   0.001   TRP B  38 
 HIS   0.005   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5842)
  covalent geometry    : angle       0.64139 ( 7902)
  hydrogen bonds       : bond        0.03426 (  221)
  hydrogen bonds       : angle       5.10589 (  600)
  metal coordination   : bond        0.00786 (    8)
  metal coordination   : angle       5.52197 (   12)

*********************** 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
  107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.8307 (mt) cc_final: 0.7957 (mt)
REVERT: A   60 LYS cc_start: 0.8583 (mttm) cc_final: 0.8308 (mtpp)
REVERT: A   99 LYS cc_start: 0.8773 (tptp) cc_final: 0.8392 (tptp)
REVERT: A  318 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6329 (m-10)
REVERT: A  401 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8235 (tm)
REVERT: A  419 LYS cc_start: 0.8475 (mttt) cc_final: 0.8122 (mtmm)
REVERT: A  433 TYR cc_start: 0.7910 (m-80) cc_final: 0.7433 (m-80)
REVERT: A  466 THR cc_start: 0.9432 (p) cc_final: 0.9197 (t)
REVERT: A  467 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8803 (mm-30)
REVERT: A  480 MET cc_start: 0.7346 (ppp) cc_final: 0.6162 (pp-130)
REVERT: A  495 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8436 (tm-30)
REVERT: A  499 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8717 (mp)
REVERT: B   92 LYS cc_start: 0.9180 (tttt) cc_final: 0.8800 (ptmm)
REVERT: B   99 LYS cc_start: 0.9158 (tppt) cc_final: 0.8796 (tptp)
REVERT: B  271 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7818 (mm-30)
REVERT: B  273 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6951 (mpt-90)
REVERT: B  325 GLU cc_start: 0.8855 (tt0) cc_final: 0.8453 (mp0)
REVERT: B  392 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7530 (mtt-85)
REVERT: B  406 MET cc_start: 0.7682 (mmm) cc_final: 0.7436 (mmm)
REVERT: B  416 MET cc_start: 0.8845 (mmt) cc_final: 0.8448 (mmp)
REVERT: B  477 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7098 (ttt-90)
  outliers start: 22
  outliers final: 9
  residues processed: 95
  average time/residue: 0.5241
  time to fit residues: 52.5036
Evaluate side-chains
  88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
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  493 SER
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  518 ASN
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  273 ARG
Chi-restraints excluded: chain B residue  460 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0264 > 50:
  distance: 15 - 37:  11.260
  distance: 22 - 49:  24.937
  distance: 25 - 29:   9.163
  distance: 26 - 58:  14.642
  distance: 29 - 30:   7.071
  distance: 30 - 31:   5.377
  distance: 30 - 33:   4.682
  distance: 31 - 32:   8.931
  distance: 31 - 37:  15.879
  distance: 33 - 34:   5.259
  distance: 34 - 35:   7.308
  distance: 34 - 36:   6.137
  distance: 37 - 38:  15.449
  distance: 38 - 39:   4.337
  distance: 38 - 41:   6.242
  distance: 39 - 40:   7.532
  distance: 39 - 49:  18.029
  distance: 40 - 74:   8.180
  distance: 41 - 42:  11.298
  distance: 42 - 43:  10.777
  distance: 42 - 44:   6.794
  distance: 43 - 45:   8.909
  distance: 44 - 46:  14.612
  distance: 45 - 47:  15.662
  distance: 46 - 47:  12.754
  distance: 47 - 48:  18.499
  distance: 49 - 50:  22.273
  distance: 50 - 51:  10.134
  distance: 50 - 53:  15.944
  distance: 51 - 52:   8.070
  distance: 51 - 58:  13.337
  distance: 52 - 82:   9.739
  distance: 53 - 54:  14.173
  distance: 54 - 55:  13.727
  distance: 55 - 56:   8.671
  distance: 55 - 57:  12.475
  distance: 58 - 59:   9.832
  distance: 59 - 60:  12.919
  distance: 59 - 62:   6.425
  distance: 60 - 61:   8.247
  distance: 60 - 66:  18.304
  distance: 62 - 63:  18.789
  distance: 63 - 64:  10.622
  distance: 63 - 65:   9.215
  distance: 66 - 67:  12.447
  distance: 67 - 68:   4.826
  distance: 67 - 70:   7.395
  distance: 68 - 69:  18.035
  distance: 68 - 74:   5.630
  distance: 70 - 71:  24.377
  distance: 71 - 72:   8.558
  distance: 71 - 73:   3.561
  distance: 74 - 75:   3.341
  distance: 75 - 76:  15.037
  distance: 75 - 78:   7.810
  distance: 76 - 77:  24.819
  distance: 76 - 82:   8.785
  distance: 78 - 79:  17.781
  distance: 78 - 80:  15.565
  distance: 79 - 81:  18.585
  distance: 82 - 83:   8.420
  distance: 83 - 84:   8.350
  distance: 83 - 86:   7.531
  distance: 84 - 85:  24.700
  distance: 84 - 90:   9.991
  distance: 86 - 87:   9.187
  distance: 87 - 88:  10.064
  distance: 87 - 89:   3.919
  distance: 90 - 91:  12.172
  distance: 91 - 92:  11.203
  distance: 91 - 94:   9.408
  distance: 92 - 93:  33.136
  distance: 92 - 101:  23.987
  distance: 94 - 95:   9.063
  distance: 95 - 96:  18.021
  distance: 96 - 97:  10.710
  distance: 97 - 98:  31.763
  distance: 98 - 99:  20.303
  distance: 98 - 100:  19.862
  distance: 101 - 102:  24.993
  distance: 102 - 103:  32.924
  distance: 103 - 104:  16.734
  distance: 103 - 105:   6.997
  distance: 105 - 106:   9.605
  distance: 106 - 107:  20.024
  distance: 106 - 109:   6.303
  distance: 107 - 108:  15.639
  distance: 107 - 119:   8.479
  distance: 109 - 110:  14.917
  distance: 110 - 111:  16.003
  distance: 110 - 112:  13.817
  distance: 111 - 113:  13.966
  distance: 112 - 114:  17.376
  distance: 112 - 115:  12.440
  distance: 113 - 114:  15.902
  distance: 114 - 116:   4.332
  distance: 115 - 117:  10.036
  distance: 116 - 118:  12.197
  distance: 117 - 118:  10.988
  distance: 215 - 220:   3.135