Starting phenix.real_space_refine
on Fri Aug 22 22:24:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w6d_37321/08_2025/8w6d_37321.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w6d_37321/08_2025/8w6d_37321.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2025/8w6d_37321.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2025/8w6d_37321.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2025/8w6d_37321.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2025/8w6d_37321.map"
  }
  resolution = 2.5
  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=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      56      5.16       5
     Na      2      4.78       5
     C    5566      2.51       5
     N    1286      2.21       5
     O    1392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 8304
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4068
          Classifications: {'peptide': 529}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 33, 'TRANS': 495}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 84
          Unusual residues: {' NA': 1, '3PH': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.60, per 1000 atoms: 0.31
  Number of scatterers: 8304
  At special positions: 0
  Unit cell: (88.047, 107.613, 89.134, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      56     16.00
     P       2     15.00
     Na      2     11.00
     O    1392      8.00
     N    1286      7.00
     C    5566      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: 0.51
  Conformation dependent library (CDL) restraints added in 405.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 2 sheets defined
      77.6% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.725A  pdb=" N   LEU A   8 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 24
      Proline residue:  A  21  - end of helix
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 33 through 52
    Processing helix  chain 'A' and resid 55 through 60
    Processing helix  chain 'A' and resid 62 through 70
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.667A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 103
      removed outlier: 3.567A  pdb=" N   VAL A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TRP A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 118
      removed outlier: 3.781A  pdb=" N   ARG A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 136
    Processing helix  chain 'A' and resid 140 through 163
      Proline residue:  A 150  - end of helix
    Processing helix  chain 'A' and resid 214 through 232
      removed outlier: 3.661A  pdb=" N   SER A 230 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 240 through 254
      removed outlier: 3.969A  pdb=" N   LEU A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 290
      Proline residue:  A 272  - end of helix
    Processing helix  chain 'A' and resid 305 through 322
      removed outlier: 3.695A  pdb=" N   GLN A 309 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA A 310 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A 322 " --> pdb=" O   GLU A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 346
      removed outlier: 3.512A  pdb=" N   THR A 345 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 358
    Processing helix  chain 'A' and resid 369 through 384
      removed outlier: 3.933A  pdb=" N   PHE A 382 " --> pdb=" O   GLY A 378 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ILE A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 417
    Processing helix  chain 'A' and resid 418 through 438
      removed outlier: 3.641A  pdb=" N   VAL A 422 " --> pdb=" O   PRO A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 447 through 453
      Proline residue:  A 450  - end of helix
      removed outlier: 4.309A  pdb=" N   SER A 453 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 447 through 453'
    Processing helix  chain 'A' and resid 455 through 474
      removed outlier: 3.625A  pdb=" N   ALA A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A 461 " --> pdb=" O   PRO A 457 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   CYS A 473 " --> pdb=" O   THR A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 494
      removed outlier: 3.655A  pdb=" N   LEU A 484 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
      Proline residue:  A 485  - end of helix
      removed outlier: 3.523A  pdb=" N   ILE A 494 " --> pdb=" O   MET A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 509
    Processing helix  chain 'A' and resid 520 through 525
      removed outlier: 3.519A  pdb=" N   VAL A 525 " --> pdb=" O   PRO A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 556
      removed outlier: 3.540A  pdb=" N   MET A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A 543 " --> pdb=" O   ALA A 539 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE A 545 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 564
    Processing helix  chain 'A' and resid 569 through 573
      removed outlier: 3.621A  pdb=" N   GLN A 573 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 11
      removed outlier: 3.726A  pdb=" N   LEU B   8 " --> pdb=" O   CYS B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 24
      Proline residue:  B  21  - end of helix
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 33 through 52
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'B' and resid 62 through 70
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.667A  pdb=" N   VAL B  80 " --> pdb=" O   SER B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 103
      removed outlier: 3.567A  pdb=" N   VAL B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TRP B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 118
      removed outlier: 3.781A  pdb=" N   ARG B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 136
    Processing helix  chain 'B' and resid 140 through 163
      Proline residue:  B 150  - end of helix
    Processing helix  chain 'B' and resid 214 through 232
      removed outlier: 3.660A  pdb=" N   SER B 230 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 240 through 254
      removed outlier: 3.968A  pdb=" N   LEU B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 290
      Proline residue:  B 272  - end of helix
    Processing helix  chain 'B' and resid 305 through 322
      removed outlier: 3.695A  pdb=" N   GLN B 309 " --> pdb=" O   GLN B 305 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA B 310 " --> pdb=" O   GLU B 306 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA B 311 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B 322 " --> pdb=" O   GLU B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 346
      removed outlier: 3.512A  pdb=" N   THR B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 358
    Processing helix  chain 'B' and resid 369 through 384
      removed outlier: 3.934A  pdb=" N   PHE B 382 " --> pdb=" O   GLY B 378 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE B 383 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 417
    Processing helix  chain 'B' and resid 418 through 438
      removed outlier: 3.641A  pdb=" N   VAL B 422 " --> pdb=" O   PRO B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 446
    Processing helix  chain 'B' and resid 447 through 453
      Proline residue:  B 450  - end of helix
      removed outlier: 4.309A  pdb=" N   SER B 453 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 447 through 453'
    Processing helix  chain 'B' and resid 455 through 474
      removed outlier: 3.625A  pdb=" N   ALA B 460 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B 461 " --> pdb=" O   PRO B 457 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   CYS B 473 " --> pdb=" O   THR B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 494
      removed outlier: 3.656A  pdb=" N   LEU B 484 " --> pdb=" O   THR B 480 " (cutoff:3.500A)
      Proline residue:  B 485  - end of helix
      removed outlier: 3.524A  pdb=" N   ILE B 494 " --> pdb=" O   MET B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 509
    Processing helix  chain 'B' and resid 520 through 525
      removed outlier: 3.519A  pdb=" N   VAL B 525 " --> pdb=" O   PRO B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 556
      removed outlier: 3.540A  pdb=" N   MET B 536 " --> pdb=" O   LYS B 532 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B 543 " --> pdb=" O   ALA B 539 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE B 545 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 564
    Processing helix  chain 'B' and resid 569 through 573
      removed outlier: 3.621A  pdb=" N   GLN B 573 " --> pdb=" O   SER B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 393
    Processing sheet with id=AA2, first strand: chain 'B' and resid 392 through 393

    501 hydrogen bonds defined for protein.
    1491 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: 1.06

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1305
        1.32 -     1.44: 2218
        1.44 -     1.56: 4915
        1.56 -     1.69: 2
        1.69 -     1.81: 92
  Bond restraints: 8532
  Sorted by residual:
  bond pdb=" O11 3PH A 802 "
       pdb=" P   3PH A 802 "
    ideal  model  delta    sigma   weight residual
    1.703  1.611  0.092 2.00e-02 2.50e+03 2.11e+01
  bond pdb=" O11 3PH B 802 "
       pdb=" P   3PH B 802 "
    ideal  model  delta    sigma   weight residual
    1.703  1.612  0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C1  3PH B 802 "
       pdb=" O11 3PH B 802 "
    ideal  model  delta    sigma   weight residual
    1.385  1.451 -0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" C1  3PH A 802 "
       pdb=" O11 3PH A 802 "
    ideal  model  delta    sigma   weight residual
    1.385  1.451 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" C   PRO B 520 "
       pdb=" N   PRO B 521 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.035 1.51e-02 4.39e+03 5.35e+00
  ... (remaining 8527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 11215
        2.50 -     5.01: 363
        5.01 -     7.51: 62
        7.51 -    10.01: 10
       10.01 -    12.51: 2
  Bond angle restraints: 11652
  Sorted by residual:
  angle pdb=" N   PRO A 520 "
        pdb=" CA  PRO A 520 "
        pdb=" C   PRO A 520 "
      ideal   model   delta    sigma   weight residual
     110.70  117.59   -6.89 1.22e+00 6.72e-01 3.19e+01
  angle pdb=" N   PRO B 520 "
        pdb=" CA  PRO B 520 "
        pdb=" C   PRO B 520 "
      ideal   model   delta    sigma   weight residual
     110.70  117.57   -6.87 1.22e+00 6.72e-01 3.17e+01
  angle pdb=" CA  THR A 519 "
        pdb=" CB  THR A 519 "
        pdb=" CG2 THR A 519 "
      ideal   model   delta    sigma   weight residual
     110.50  118.13   -7.63 1.70e+00 3.46e-01 2.02e+01
  angle pdb=" CA  THR B 519 "
        pdb=" CB  THR B 519 "
        pdb=" CG2 THR B 519 "
      ideal   model   delta    sigma   weight residual
     110.50  118.10   -7.60 1.70e+00 3.46e-01 2.00e+01
  angle pdb=" C   SER A 557 "
        pdb=" N   TRP A 558 "
        pdb=" CA  TRP A 558 "
      ideal   model   delta    sigma   weight residual
     121.54  128.87   -7.33 1.91e+00 2.74e-01 1.47e+01
  ... (remaining 11647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 4634
       17.13 -    34.25: 370
       34.25 -    51.38: 80
       51.38 -    68.51: 14
       68.51 -    85.63: 8
  Dihedral angle restraints: 5106
    sinusoidal: 2050
      harmonic: 3056
  Sorted by residual:
  dihedral pdb=" CA  GLU A 302 "
           pdb=" C   GLU A 302 "
           pdb=" N   LYS A 303 "
           pdb=" CA  LYS A 303 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.82  -20.18     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  GLU B 302 "
           pdb=" C   GLU B 302 "
           pdb=" N   LYS B 303 "
           pdb=" CA  LYS B 303 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.91  -20.09     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  ALA B 512 "
           pdb=" C   ALA B 512 "
           pdb=" N   PHE B 513 "
           pdb=" CA  PHE B 513 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.97  -19.03     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 5103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1049
       0.062 -    0.124: 276
       0.124 -    0.185: 52
       0.185 -    0.247: 11
       0.247 -    0.309: 4
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CA  THR A 519 "
            pdb=" N   THR A 519 "
            pdb=" C   THR A 519 "
            pdb=" CB  THR A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.22    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  THR B 519 "
            pdb=" N   THR B 519 "
            pdb=" C   THR B 519 "
            pdb=" CB  THR B 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.22    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CBE Y01 A 803 "
            pdb=" CAP Y01 A 803 "
            pdb=" CBB Y01 A 803 "
            pdb=" CBI Y01 A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.32    0.25 2.00e-01 2.50e+01 1.57e+00
  ... (remaining 1389 not shown)

  Planarity restraints: 1402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  25 "   -0.045 5.00e-02 4.00e+02   6.71e-02 7.20e+00
        pdb=" N   PRO B  26 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B  26 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B  26 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  25 "    0.045 5.00e-02 4.00e+02   6.71e-02 7.20e+00
        pdb=" N   PRO A  26 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A  26 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  26 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  67 "   -0.044 5.00e-02 4.00e+02   6.59e-02 6.95e+00
        pdb=" N   PRO A  68 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1399 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 2962
        2.89 -     3.39: 8074
        3.39 -     3.90: 13776
        3.90 -     4.40: 15511
        4.40 -     4.90: 26347
  Nonbonded interactions: 66670
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 467 "
            pdb=" OG1 THR A 471 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" O   VAL B 467 "
            pdb=" OG1 THR B 471 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" OG  SER B  33 "
            pdb=" OE1 GLU B  35 "
     model   vdw
     2.414 3.040
  nonbonded pdb=" OG  SER A  33 "
            pdb=" OE1 GLU A  35 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" O   TRP A   9 "
            pdb=" NH1 ARG A  12 "
     model   vdw
     2.422 3.120
  ... (remaining 66665 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: 0.02
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:             1.100
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.240
  Find NCS groups from input model:        0.060
  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:6.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.092   8532  Z= 0.371
  Angle     :  1.076  12.515  11652  Z= 0.580
  Chirality :  0.062   0.309   1392
  Planarity :  0.009   0.067   1402
  Dihedral  : 13.667  85.633   3122
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.95 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.85 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.77 (0.22), residues: 1050
  helix: -1.06 (0.16), residues: 726
  sheet: -4.33 (0.46), residues: 20
  loop : -3.36 (0.30), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 112 
 TYR   0.011   0.002   TYR A 500 
 PHE   0.043   0.003   PHE B 344 
 TRP   0.037   0.003   TRP A 410 
 HIS   0.008   0.002   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00911 ( 8532)
  covalent geometry    : angle       1.07573 (11652)
  hydrogen bonds       : bond        0.17338 (  501)
  hydrogen bonds       : angle       5.43743 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A   70 MET cc_start: 0.8160 (mtm) cc_final: 0.7951 (mtp)
REVERT: A  137 MET cc_start: 0.8884 (mtp) cc_final: 0.8647 (mtp)
REVERT: A  303 LYS cc_start: 0.7143 (tttm) cc_final: 0.6850 (tttp)
REVERT: A  318 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7399 (tp30)
REVERT: A  344 PHE cc_start: 0.7876 (m-80) cc_final: 0.7605 (t80)
REVERT: A  417 MET cc_start: 0.9113 (tpp) cc_final: 0.8862 (tpp)
REVERT: A  490 MET cc_start: 0.8214 (tmm) cc_final: 0.7771 (tmm)
REVERT: B   70 MET cc_start: 0.8159 (mtm) cc_final: 0.7922 (mtp)
REVERT: B  137 MET cc_start: 0.8883 (mtp) cc_final: 0.8651 (mtp)
REVERT: B  303 LYS cc_start: 0.7133 (tttm) cc_final: 0.6840 (tttp)
REVERT: B  318 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7406 (tp30)
REVERT: B  344 PHE cc_start: 0.7877 (m-80) cc_final: 0.7606 (t80)
REVERT: B  417 MET cc_start: 0.9113 (tpp) cc_final: 0.8870 (tpp)
REVERT: B  490 MET cc_start: 0.8214 (tmm) cc_final: 0.7769 (tmm)
  outliers start: 2
  outliers final: 2
  residues processed: 126
  average time/residue: 0.6512
  time to fit residues: 85.9873
Evaluate side-chains
  100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue  517 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A 243 ASN
A 257 ASN
A 297 ASN
A 305 GLN
A 319 HIS
A 356 ASN
A 397 ASN
A 414 ASN
B 243 ASN
B 257 ASN
B 297 ASN
B 305 GLN
B 356 ASN
B 397 ASN
B 414 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.116459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.092357 restraints weight = 9591.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.42
r_work: 0.2849 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8532  Z= 0.137
  Angle     :  0.628   7.621  11652  Z= 0.324
  Chirality :  0.042   0.174   1392
  Planarity :  0.006   0.056   1402
  Dihedral  :  9.604  58.213   1322
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  8.45 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.27 (0.26), residues: 1050
  helix:  0.91 (0.19), residues: 746
  sheet: -4.22 (0.48), residues: 20
  loop : -2.85 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 295 
 TYR   0.005   0.001   TYR B  11 
 PHE   0.016   0.002   PHE B 344 
 TRP   0.023   0.002   TRP A 558 
 HIS   0.002   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8532)
  covalent geometry    : angle       0.62781 (11652)
  hydrogen bonds       : bond        0.05648 (  501)
  hydrogen bonds       : angle       3.98342 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  163 GLN cc_start: 0.7856 (mt0) cc_final: 0.7576 (mt0)
REVERT: A  256 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7058 (pt0)
REVERT: A  303 LYS cc_start: 0.7232 (tttm) cc_final: 0.6466 (ttpp)
REVERT: A  304 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7490 (mmt)
REVERT: A  318 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7984 (tp30)
REVERT: A  325 MET cc_start: 0.9105 (mtp) cc_final: 0.8892 (mtp)
REVERT: A  490 MET cc_start: 0.8645 (tmm) cc_final: 0.8253 (tmm)
REVERT: B   52 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7847 (tp30)
REVERT: B  163 GLN cc_start: 0.7861 (mt0) cc_final: 0.7584 (mt0)
REVERT: B  256 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7053 (pt0)
REVERT: B  303 LYS cc_start: 0.7226 (tttm) cc_final: 0.6467 (ttpp)
REVERT: B  304 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7494 (mmt)
REVERT: B  318 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7970 (tp30)
REVERT: B  325 MET cc_start: 0.9109 (mtp) cc_final: 0.8897 (mtp)
REVERT: B  490 MET cc_start: 0.8650 (tmm) cc_final: 0.8259 (tmm)
  outliers start: 12
  outliers final: 2
  residues processed: 113
  average time/residue: 0.5451
  time to fit residues: 65.1750
Evaluate side-chains
  101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue  256 GLN
Chi-restraints excluded: chain B residue  304 MET
Chi-restraints excluded: chain B residue  517 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0980
   chunk 64 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0870
   chunk 52 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0370
   overall best weight:    0.3436

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
B 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.121592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.098431 restraints weight = 9529.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.37
r_work: 0.2948 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8532  Z= 0.113
  Angle     :  0.560   6.875  11652  Z= 0.287
  Chirality :  0.040   0.153   1392
  Planarity :  0.005   0.058   1402
  Dihedral  :  9.203  57.919   1322
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  8.56 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.89 (0.27), residues: 1050
  helix:  1.87 (0.19), residues: 748
  sheet: -4.03 (0.55), residues: 20
  loop : -2.71 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 320 
 TYR   0.005   0.001   TYR B  40 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.017   0.001   TRP B 410 
 HIS   0.002   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 8532)
  covalent geometry    : angle       0.56036 (11652)
  hydrogen bonds       : bond        0.03843 (  501)
  hydrogen bonds       : angle       3.59066 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   70 MET cc_start: 0.8738 (mtm) cc_final: 0.8413 (mtp)
REVERT: A  163 GLN cc_start: 0.7466 (mt0) cc_final: 0.7201 (mt0)
REVERT: A  303 LYS cc_start: 0.7143 (tttm) cc_final: 0.6749 (tttp)
REVERT: A  304 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7451 (mmt)
REVERT: A  490 MET cc_start: 0.8606 (tmm) cc_final: 0.8352 (tmm)
REVERT: B   70 MET cc_start: 0.8738 (mtm) cc_final: 0.8414 (mtp)
REVERT: B  163 GLN cc_start: 0.7470 (mt0) cc_final: 0.7210 (mt0)
REVERT: B  303 LYS cc_start: 0.7131 (tttm) cc_final: 0.6740 (tttp)
REVERT: B  304 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7429 (mmt)
REVERT: B  490 MET cc_start: 0.8607 (tmm) cc_final: 0.8353 (tmm)
  outliers start: 18
  outliers final: 4
  residues processed: 110
  average time/residue: 0.5480
  time to fit residues: 63.8340
Evaluate side-chains
  105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  304 MET
Chi-restraints excluded: chain B residue  517 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.117491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.093703 restraints weight = 9716.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.39
r_work: 0.2870 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8532  Z= 0.141
  Angle     :  0.622   9.114  11652  Z= 0.311
  Chirality :  0.043   0.165   1392
  Planarity :  0.005   0.060   1402
  Dihedral  :  9.452  59.325   1322
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.05 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.23 (0.28), residues: 1050
  helix:  2.10 (0.20), residues: 748
  sheet: -4.07 (0.55), residues: 20
  loop : -2.53 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 320 
 TYR   0.008   0.001   TYR B 500 
 PHE   0.014   0.001   PHE A 528 
 TRP   0.020   0.002   TRP A 410 
 HIS   0.003   0.001   HIS B 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8532)
  covalent geometry    : angle       0.62222 (11652)
  hydrogen bonds       : bond        0.05271 (  501)
  hydrogen bonds       : angle       3.61924 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   70 MET cc_start: 0.8762 (mtm) cc_final: 0.8408 (mtp)
REVERT: A  163 GLN cc_start: 0.7551 (mt0) cc_final: 0.7256 (mt0)
REVERT: A  303 LYS cc_start: 0.6978 (tttm) cc_final: 0.6644 (tttp)
REVERT: A  490 MET cc_start: 0.8580 (tmm) cc_final: 0.8346 (tmm)
REVERT: B   70 MET cc_start: 0.8761 (mtm) cc_final: 0.8413 (mtp)
REVERT: B  163 GLN cc_start: 0.7544 (mt0) cc_final: 0.7254 (mt0)
REVERT: B  303 LYS cc_start: 0.6981 (tttm) cc_final: 0.6649 (tttp)
REVERT: B  490 MET cc_start: 0.8595 (tmm) cc_final: 0.8363 (tmm)
  outliers start: 18
  outliers final: 8
  residues processed: 106
  average time/residue: 0.4936
  time to fit residues: 55.3596
Evaluate side-chains
  102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  517 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0870
   chunk 31 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.7158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.118927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.095405 restraints weight = 9684.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.37
r_work: 0.2884 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8532  Z= 0.122
  Angle     :  0.587   7.934  11652  Z= 0.296
  Chirality :  0.042   0.234   1392
  Planarity :  0.005   0.061   1402
  Dihedral  :  9.366  57.838   1322
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  9.59 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.47 (0.28), residues: 1050
  helix:  2.29 (0.20), residues: 748
  sheet: -4.04 (0.56), residues: 20
  loop : -2.45 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 320 
 TYR   0.006   0.001   TYR B  40 
 PHE   0.011   0.001   PHE B 568 
 TRP   0.020   0.001   TRP A 410 
 HIS   0.001   0.001   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8532)
  covalent geometry    : angle       0.58746 (11652)
  hydrogen bonds       : bond        0.04517 (  501)
  hydrogen bonds       : angle       3.54346 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  163 GLN cc_start: 0.7451 (mt0) cc_final: 0.7130 (mt0)
REVERT: A  303 LYS cc_start: 0.6935 (tttm) cc_final: 0.6598 (tttp)
REVERT: A  304 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7418 (mmt)
REVERT: A  490 MET cc_start: 0.8544 (tmm) cc_final: 0.8298 (tmm)
REVERT: B  163 GLN cc_start: 0.7448 (mt0) cc_final: 0.7130 (mt0)
REVERT: B  303 LYS cc_start: 0.6929 (tttm) cc_final: 0.6598 (tttp)
REVERT: B  304 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7423 (mmt)
REVERT: B  490 MET cc_start: 0.8561 (tmm) cc_final: 0.8318 (tmm)
  outliers start: 23
  outliers final: 12
  residues processed: 110
  average time/residue: 0.5061
  time to fit residues: 58.7331
Evaluate side-chains
  110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  304 MET
Chi-restraints excluded: chain B residue  517 VAL
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
A 393 GLN
B 393 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.113593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.089838 restraints weight = 9550.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.37
r_work: 0.2812 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   8532  Z= 0.231
  Angle     :  0.749   9.701  11652  Z= 0.376
  Chirality :  0.049   0.225   1392
  Planarity :  0.006   0.060   1402
  Dihedral  : 10.384  57.830   1322
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.19 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  :  9.93 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.01 (0.27), residues: 1050
  helix:  1.69 (0.19), residues: 768
  sheet: -3.77 (0.61), residues: 20
  loop : -2.10 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  12 
 TYR   0.013   0.002   TYR B 500 
 PHE   0.023   0.003   PHE A 528 
 TRP   0.026   0.003   TRP A 410 
 HIS   0.005   0.001   HIS B 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 8532)
  covalent geometry    : angle       0.74949 (11652)
  hydrogen bonds       : bond        0.07456 (  501)
  hydrogen bonds       : angle       3.86210 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8381 (t80) cc_final: 0.7729 (m-80)
REVERT: A   70 MET cc_start: 0.8835 (mtm) cc_final: 0.8521 (mtp)
REVERT: A  163 GLN cc_start: 0.7697 (mt0) cc_final: 0.7400 (mt0)
REVERT: A  295 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7679 (mtp180)
REVERT: A  303 LYS cc_start: 0.6972 (tttm) cc_final: 0.6583 (tttp)
REVERT: B   18 PHE cc_start: 0.8368 (t80) cc_final: 0.7728 (m-80)
REVERT: B   70 MET cc_start: 0.8841 (mtm) cc_final: 0.8531 (mtp)
REVERT: B  163 GLN cc_start: 0.7704 (mt0) cc_final: 0.7414 (mt0)
REVERT: B  295 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7770 (mtp180)
REVERT: B  303 LYS cc_start: 0.6974 (tttm) cc_final: 0.6588 (tttp)
  outliers start: 21
  outliers final: 12
  residues processed: 106
  average time/residue: 0.5080
  time to fit residues: 56.8674
Evaluate side-chains
  108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  295 ARG
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  517 VAL
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0270
   chunk 100 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
B 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.117923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.094503 restraints weight = 9713.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 1.37
r_work: 0.2874 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8532  Z= 0.126
  Angle     :  0.599   7.836  11652  Z= 0.303
  Chirality :  0.042   0.217   1392
  Planarity :  0.005   0.058   1402
  Dihedral  :  9.890  57.637   1322
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.07 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.52 (0.28), residues: 1050
  helix:  2.14 (0.19), residues: 772
  sheet: -3.83 (0.66), residues: 20
  loop : -2.26 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 320 
 TYR   0.007   0.001   TYR A  40 
 PHE   0.012   0.001   PHE A 568 
 TRP   0.022   0.002   TRP A 410 
 HIS   0.002   0.001   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8532)
  covalent geometry    : angle       0.59892 (11652)
  hydrogen bonds       : bond        0.04765 (  501)
  hydrogen bonds       : angle       3.63705 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8280 (t80) cc_final: 0.7699 (m-80)
REVERT: A   70 MET cc_start: 0.8778 (mtm) cc_final: 0.8515 (mtp)
REVERT: A  163 GLN cc_start: 0.7504 (mt0) cc_final: 0.7157 (mt0)
REVERT: A  303 LYS cc_start: 0.6921 (tttm) cc_final: 0.6523 (tttp)
REVERT: B   18 PHE cc_start: 0.8257 (t80) cc_final: 0.7679 (m-80)
REVERT: B   70 MET cc_start: 0.8779 (mtm) cc_final: 0.8518 (mtp)
REVERT: B  163 GLN cc_start: 0.7509 (mt0) cc_final: 0.7166 (mt0)
REVERT: B  303 LYS cc_start: 0.6925 (tttm) cc_final: 0.6533 (tttp)
  outliers start: 13
  outliers final: 10
  residues processed: 103
  average time/residue: 0.5055
  time to fit residues: 54.9832
Evaluate side-chains
  102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  517 VAL
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 51 optimal weight:    0.3980
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
B 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.117860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.094303 restraints weight = 9637.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.38
r_work: 0.2868 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8532  Z= 0.131
  Angle     :  0.603   7.977  11652  Z= 0.305
  Chirality :  0.043   0.225   1392
  Planarity :  0.005   0.058   1402
  Dihedral  :  9.763  56.554   1322
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.84 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.62 (0.28), residues: 1050
  helix:  2.21 (0.19), residues: 772
  sheet: -3.72 (0.68), residues: 20
  loop : -2.22 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 320 
 TYR   0.006   0.001   TYR B  40 
 PHE   0.012   0.001   PHE B 568 
 TRP   0.023   0.002   TRP A 410 
 HIS   0.002   0.001   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8532)
  covalent geometry    : angle       0.60301 (11652)
  hydrogen bonds       : bond        0.04877 (  501)
  hydrogen bonds       : angle       3.58624 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8241 (t80) cc_final: 0.7649 (m-80)
REVERT: A   70 MET cc_start: 0.8756 (mtm) cc_final: 0.8513 (mtp)
REVERT: A  163 GLN cc_start: 0.7447 (mt0) cc_final: 0.7086 (mt0)
REVERT: A  303 LYS cc_start: 0.6854 (tttm) cc_final: 0.6446 (tttp)
REVERT: B   18 PHE cc_start: 0.8230 (t80) cc_final: 0.7680 (m-80)
REVERT: B   70 MET cc_start: 0.8774 (mtm) cc_final: 0.8534 (mtp)
REVERT: B  163 GLN cc_start: 0.7436 (mt0) cc_final: 0.7077 (mt0)
REVERT: B  295 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7719 (mtp180)
REVERT: B  303 LYS cc_start: 0.6853 (tttm) cc_final: 0.6448 (tttp)
  outliers start: 15
  outliers final: 12
  residues processed: 104
  average time/residue: 0.5243
  time to fit residues: 57.7162
Evaluate side-chains
  105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  517 VAL
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0970
   chunk 37 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0270
   chunk 52 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5236

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.120327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.096993 restraints weight = 9703.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.38
r_work: 0.2938 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8532  Z= 0.118
  Angle     :  0.574   7.420  11652  Z= 0.291
  Chirality :  0.042   0.237   1392
  Planarity :  0.005   0.058   1402
  Dihedral  :  9.448  56.202   1322
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.76 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.73 (0.28), residues: 1050
  helix:  2.45 (0.19), residues: 756
  sheet: -3.67 (0.68), residues: 20
  loop : -2.42 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 320 
 TYR   0.007   0.001   TYR B  40 
 PHE   0.010   0.001   PHE B 351 
 TRP   0.021   0.001   TRP A 410 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8532)
  covalent geometry    : angle       0.57446 (11652)
  hydrogen bonds       : bond        0.04059 (  501)
  hydrogen bonds       : angle       3.51159 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8221 (t80) cc_final: 0.7634 (m-80)
REVERT: A  163 GLN cc_start: 0.7286 (mt0) cc_final: 0.7024 (mt0)
REVERT: A  303 LYS cc_start: 0.6822 (tttm) cc_final: 0.6420 (tttp)
REVERT: B   18 PHE cc_start: 0.8215 (t80) cc_final: 0.7666 (m-80)
REVERT: B   70 MET cc_start: 0.8650 (mtm) cc_final: 0.8446 (mtp)
REVERT: B  163 GLN cc_start: 0.7293 (mt0) cc_final: 0.7037 (mt0)
REVERT: B  303 LYS cc_start: 0.6817 (tttm) cc_final: 0.6419 (tttp)
  outliers start: 16
  outliers final: 8
  residues processed: 113
  average time/residue: 0.5044
  time to fit residues: 60.3928
Evaluate side-chains
  107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  517 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 72 optimal weight:    0.1980
   chunk 4 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 70 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0050
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 446 ASN
B 393 GLN
B 446 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.120653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.097426 restraints weight = 9645.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.37
r_work: 0.2943 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8532  Z= 0.119
  Angle     :  0.577   7.459  11652  Z= 0.292
  Chirality :  0.042   0.239   1392
  Planarity :  0.005   0.059   1402
  Dihedral  :  9.332  56.042   1322
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.21 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.85 (0.28), residues: 1050
  helix:  2.52 (0.19), residues: 748
  sheet: -3.40 (0.73), residues: 20
  loop : -2.20 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 320 
 TYR   0.007   0.001   TYR B  40 
 PHE   0.010   0.001   PHE B 351 
 TRP   0.021   0.001   TRP A 410 
 HIS   0.004   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8532)
  covalent geometry    : angle       0.57726 (11652)
  hydrogen bonds       : bond        0.04143 (  501)
  hydrogen bonds       : angle       3.47817 ( 1491)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8182 (t80) cc_final: 0.7595 (m-80)
REVERT: A  256 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6713 (pm20)
REVERT: A  303 LYS cc_start: 0.6824 (tttm) cc_final: 0.6434 (tttp)
REVERT: A  304 MET cc_start: 0.7760 (mmm) cc_final: 0.7448 (mmt)
REVERT: B   18 PHE cc_start: 0.8176 (t80) cc_final: 0.7630 (m-80)
REVERT: B  256 GLN cc_start: 0.7064 (pm20) cc_final: 0.6727 (pm20)
REVERT: B  295 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7589 (mtp180)
REVERT: B  303 LYS cc_start: 0.6825 (tttm) cc_final: 0.6440 (tttp)
REVERT: B  304 MET cc_start: 0.7771 (mmm) cc_final: 0.7456 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 108
  average time/residue: 0.4675
  time to fit residues: 53.4951
Evaluate side-chains
  110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  295 ARG
Chi-restraints excluded: chain B residue  517 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 68 optimal weight:    0.2980
   chunk 43 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 163 GLN
B 163 GLN
B 393 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.118430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.094921 restraints weight = 9642.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.37
r_work: 0.2901 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8532  Z= 0.134
  Angle     :  0.609   7.869  11652  Z= 0.307
  Chirality :  0.043   0.229   1392
  Planarity :  0.005   0.060   1402
  Dihedral  :  9.523  56.851   1322
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.10 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.72 (0.28), residues: 1050
  helix:  2.37 (0.19), residues: 760
  sheet: -3.45 (0.75), residues: 20
  loop : -2.28 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 320 
 TYR   0.007   0.001   TYR A 500 
 PHE   0.013   0.001   PHE B 568 
 TRP   0.021   0.002   TRP A 410 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8532)
  covalent geometry    : angle       0.60858 (11652)
  hydrogen bonds       : bond        0.04950 (  501)
  hydrogen bonds       : angle       3.53103 ( 1491)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2656.53 seconds
wall clock time: 45 minutes 49.34 seconds (2749.34 seconds total)