Starting phenix.real_space_refine
on Sat Jun  7 00:12:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w6d_37321/06_2025/8w6d_37321.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w6d_37321/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w6d_37321/06_2025/8w6d_37321.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w6d_37321/06_2025/8w6d_37321.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w6d_37321/06_2025/8w6d_37321.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w6d_37321/06_2025/8w6d_37321.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.76, per 1000 atoms: 0.93
  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: 2.35
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.01
  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: 2.29

  Time building geometry restraints manager: 2.73 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: 0.04
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:             1.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.440
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.960
-------------------------------------------------------------------------------
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 : 1.35
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (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
 TRP   0.037   0.003   TRP A 410 
 HIS   0.008   0.002   HIS A 566 
 PHE   0.043   0.003   PHE B 344 
 TYR   0.011   0.002   TYR A 500 
 ARG   0.006   0.001   ARG A 112 

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

*********************** 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  : 0.870 
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: 1.5392
  time to fit residues: 203.9126
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  : 0.845 
-------------------------------------------------------------------------------
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 87 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0670
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.6920

-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.116958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.093043 restraints weight = 9461.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 1.38
r_work: 0.2856 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8532  Z= 0.133
  Angle     :  0.622   7.611  11652  Z= 0.321
  Chirality :  0.042   0.170   1392
  Planarity :  0.006   0.057   1402
  Dihedral  :  9.602  58.437   1322
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.79 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1050
  helix:  0.97 (0.19), residues: 748
  sheet: -4.19 (0.48), residues: 20
  loop : -2.87 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 558 
 HIS   0.002   0.001   HIS B 566 
 PHE   0.015   0.001   PHE A 344 
 TYR   0.005   0.001   TYR B  11 
 ARG   0.001   0.000   ARG A 538 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05373 (  501)
  hydrogen bonds       : angle       3.95304 ( 1491)
  covalent geometry    : bond        0.00282 ( 8532)
  covalent geometry    : angle       0.62197 (11652)

*********************** 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: 10
    poor density    : 109
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A  163 GLN cc_start: 0.7748 (mt0) cc_final: 0.7463 (mt0)
REVERT: A  303 LYS cc_start: 0.7224 (tttm) cc_final: 0.6458 (ttpp)
REVERT: A  318 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7983 (tp30)
REVERT: A  325 MET cc_start: 0.9093 (mtp) cc_final: 0.8876 (mtp)
REVERT: A  490 MET cc_start: 0.8631 (tmm) cc_final: 0.8235 (tmm)
REVERT: B   52 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7878 (tp30)
REVERT: B  163 GLN cc_start: 0.7753 (mt0) cc_final: 0.7471 (mt0)
REVERT: B  303 LYS cc_start: 0.7219 (tttm) cc_final: 0.6460 (ttpp)
REVERT: B  318 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7972 (tp30)
REVERT: B  325 MET cc_start: 0.9094 (mtp) cc_final: 0.8880 (mtp)
REVERT: B  490 MET cc_start: 0.8643 (tmm) cc_final: 0.8249 (tmm)
  outliers start: 10
  outliers final: 4
  residues processed: 113
  average time/residue: 1.3197
  time to fit residues: 158.2921
Evaluate side-chains
  100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue  256 GLN
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 84 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 86 optimal weight:    0.0670
   chunk 64 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.3724

-------------------------------------------------------------------------------
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 = 0.3298 r_free = 0.3298 target = 0.115237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.091173 restraints weight = 9668.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.41
r_work: 0.2828 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8532  Z= 0.154
  Angle     :  0.644   8.223  11652  Z= 0.329
  Chirality :  0.044   0.186   1392
  Planarity :  0.006   0.058   1402
  Dihedral  :  9.783  57.926   1322
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  :  8.22 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.27), residues: 1050
  helix:  1.61 (0.20), residues: 756
  sheet: -4.07 (0.51), residues: 20
  loop : -2.46 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 410 
 HIS   0.004   0.001   HIS B 566 
 PHE   0.016   0.002   PHE A 568 
 TYR   0.009   0.001   TYR B 500 
 ARG   0.002   0.000   ARG A 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06128 (  501)
  hydrogen bonds       : angle       3.79820 ( 1491)
  covalent geometry    : bond        0.00347 ( 8532)
  covalent geometry    : angle       0.64395 (11652)

*********************** 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
  123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A   70 MET cc_start: 0.8754 (mtm) cc_final: 0.8390 (mtp)
REVERT: A  163 GLN cc_start: 0.7719 (mt0) cc_final: 0.7412 (mt0)
REVERT: A  295 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7595 (mtp85)
REVERT: A  303 LYS cc_start: 0.7224 (tttm) cc_final: 0.6804 (tttp)
REVERT: A  304 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7458 (mmt)
REVERT: A  318 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7867 (tp30)
REVERT: A  490 MET cc_start: 0.8642 (tmm) cc_final: 0.8348 (tmm)
REVERT: B   52 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7827 (tp30)
REVERT: B   70 MET cc_start: 0.8759 (mtm) cc_final: 0.8397 (mtp)
REVERT: B  163 GLN cc_start: 0.7718 (mt0) cc_final: 0.7415 (mt0)
REVERT: B  295 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7765 (mtp180)
REVERT: B  303 LYS cc_start: 0.7217 (tttm) cc_final: 0.6802 (tttp)
REVERT: B  304 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7469 (mmt)
REVERT: B  318 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7881 (tp30)
REVERT: B  490 MET cc_start: 0.8648 (tmm) cc_final: 0.8357 (tmm)
  outliers start: 21
  outliers final: 9
  residues processed: 113
  average time/residue: 1.3393
  time to fit residues: 160.3900
Evaluate side-chains
  115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  295 ARG
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  393 GLN
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  295 ARG
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 57 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   overall best weight:    1.3388

-------------------------------------------------------------------------------
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 = 0.3303 r_free = 0.3303 target = 0.115581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.091536 restraints weight = 9611.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.42
r_work: 0.2834 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1678

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= 0.149
  Angle     :  0.648   9.681  11652  Z= 0.325
  Chirality :  0.044   0.212   1392
  Planarity :  0.006   0.059   1402
  Dihedral  :  9.920  59.628   1322
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  :  8.90 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 1050
  helix:  1.83 (0.19), residues: 756
  sheet: -3.90 (0.56), residues: 20
  loop : -2.35 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 410 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.016   0.002   PHE A 568 
 TYR   0.008   0.001   TYR A 500 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05801 (  501)
  hydrogen bonds       : angle       3.76223 ( 1491)
  covalent geometry    : bond        0.00337 ( 8532)
  covalent geometry    : angle       0.64777 (11652)

*********************** 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
  125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  163 GLN cc_start: 0.7623 (mt0) cc_final: 0.7273 (mt0)
REVERT: A  295 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7539 (mtp85)
REVERT: A  303 LYS cc_start: 0.7022 (tttm) cc_final: 0.6650 (tttp)
REVERT: A  304 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7450 (mmt)
REVERT: A  318 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7880 (tp30)
REVERT: A  490 MET cc_start: 0.8618 (tmm) cc_final: 0.8407 (tmm)
REVERT: B   52 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7848 (tp30)
REVERT: B   85 ASP cc_start: 0.8209 (t70) cc_final: 0.7975 (t70)
REVERT: B  163 GLN cc_start: 0.7638 (mt0) cc_final: 0.7294 (mt0)
REVERT: B  295 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7558 (mtp85)
REVERT: B  303 LYS cc_start: 0.7020 (tttm) cc_final: 0.6653 (tttp)
REVERT: B  304 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7457 (mmt)
REVERT: B  318 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7901 (tp30)
REVERT: B  490 MET cc_start: 0.8613 (tmm) cc_final: 0.8402 (tmm)
  outliers start: 26
  outliers final: 12
  residues processed: 112
  average time/residue: 1.2387
  time to fit residues: 147.5916
Evaluate side-chains
  113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  295 ARG
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  393 GLN
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  295 ARG
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 88 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.116515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.092579 restraints weight = 9544.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 1.41
r_work: 0.2867 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1789

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= 0.137
  Angle     :  0.618   7.985  11652  Z= 0.312
  Chirality :  0.043   0.220   1392
  Planarity :  0.005   0.059   1402
  Dihedral  :  9.882  58.442   1322
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.25 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.28), residues: 1050
  helix:  2.05 (0.19), residues: 760
  sheet: -3.80 (0.62), residues: 20
  loop : -2.30 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 410 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.014   0.001   PHE A 568 
 TYR   0.007   0.001   TYR B 500 
 ARG   0.002   0.000   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05288 (  501)
  hydrogen bonds       : angle       3.66054 ( 1491)
  covalent geometry    : bond        0.00303 ( 8532)
  covalent geometry    : angle       0.61828 (11652)

*********************** 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: 19
    poor density    : 99
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A   70 MET cc_start: 0.8791 (mtm) cc_final: 0.8425 (mtp)
REVERT: A  163 GLN cc_start: 0.7562 (mt0) cc_final: 0.7240 (mt0)
REVERT: A  303 LYS cc_start: 0.6968 (tttm) cc_final: 0.6582 (tttp)
REVERT: A  304 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7503 (mmt)
REVERT: A  318 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7930 (tp30)
REVERT: A  490 MET cc_start: 0.8577 (tmm) cc_final: 0.8375 (tmm)
REVERT: B   18 PHE cc_start: 0.8327 (t80) cc_final: 0.7653 (m-80)
REVERT: B   70 MET cc_start: 0.8801 (mtm) cc_final: 0.8435 (mtp)
REVERT: B   85 ASP cc_start: 0.8160 (t70) cc_final: 0.7941 (t70)
REVERT: B  163 GLN cc_start: 0.7552 (mt0) cc_final: 0.7232 (mt0)
REVERT: B  256 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7095 (pm20)
REVERT: B  303 LYS cc_start: 0.6956 (tttm) cc_final: 0.6576 (tttp)
REVERT: B  304 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7516 (mmt)
REVERT: B  490 MET cc_start: 0.8569 (tmm) cc_final: 0.8362 (tmm)
  outliers start: 19
  outliers final: 10
  residues processed: 107
  average time/residue: 1.8342
  time to fit residues: 208.7356
Evaluate side-chains
  109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 3.175 
-------------------------------------------------------------------------------
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  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  256 GLN
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 44 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.5386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.115005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.090951 restraints weight = 9595.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.41
r_work: 0.2821 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8532  Z= 0.160
  Angle     :  0.660   8.750  11652  Z= 0.331
  Chirality :  0.045   0.214   1392
  Planarity :  0.006   0.059   1402
  Dihedral  : 10.175  56.523   1322
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.13 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.27), residues: 1050
  helix:  2.00 (0.19), residues: 756
  sheet: -3.67 (0.65), residues: 20
  loop : -2.17 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 410 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.018   0.002   PHE B 568 
 TYR   0.010   0.001   TYR B 500 
 ARG   0.002   0.001   ARG B 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06119 (  501)
  hydrogen bonds       : angle       3.73892 ( 1491)
  covalent geometry    : bond        0.00368 ( 8532)
  covalent geometry    : angle       0.65981 (11652)

*********************** 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
  114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8357 (t80) cc_final: 0.7686 (m-80)
REVERT: A  163 GLN cc_start: 0.7596 (mt0) cc_final: 0.7312 (mt0)
REVERT: A  295 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7708 (mtp180)
REVERT: A  303 LYS cc_start: 0.6956 (tttm) cc_final: 0.6566 (tttp)
REVERT: A  304 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7421 (mmt)
REVERT: A  318 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7889 (tp30)
REVERT: B   18 PHE cc_start: 0.8293 (t80) cc_final: 0.7654 (m-80)
REVERT: B   85 ASP cc_start: 0.8112 (t70) cc_final: 0.7905 (t70)
REVERT: B  163 GLN cc_start: 0.7600 (mt0) cc_final: 0.7321 (mt0)
REVERT: B  295 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7568 (mtp85)
REVERT: B  303 LYS cc_start: 0.6962 (tttm) cc_final: 0.6577 (tttp)
REVERT: B  304 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7434 (mmt)
  outliers start: 19
  outliers final: 11
  residues processed: 104
  average time/residue: 1.2992
  time to fit residues: 143.2724
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  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  295 ARG
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  295 ARG
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.114758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.091101 restraints weight = 9603.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 1.36
r_work: 0.2815 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8532  Z= 0.173
  Angle     :  0.677   8.808  11652  Z= 0.340
  Chirality :  0.046   0.216   1392
  Planarity :  0.006   0.059   1402
  Dihedral  : 10.503  58.835   1322
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.00 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  9.47 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.27), residues: 1050
  helix:  1.94 (0.19), residues: 756
  sheet: -3.55 (0.67), residues: 20
  loop : -2.14 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 410 
 HIS   0.003   0.001   HIS B 566 
 PHE   0.020   0.002   PHE A 568 
 TYR   0.010   0.002   TYR A 500 
 ARG   0.002   0.001   ARG B 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06457 (  501)
  hydrogen bonds       : angle       3.78808 ( 1491)
  covalent geometry    : bond        0.00406 ( 8532)
  covalent geometry    : angle       0.67660 (11652)

*********************** 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
  118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8284 (t80) cc_final: 0.7740 (m-80)
REVERT: A   70 MET cc_start: 0.8773 (mtm) cc_final: 0.8433 (mtp)
REVERT: A  163 GLN cc_start: 0.7674 (mt0) cc_final: 0.7329 (mt0)
REVERT: A  295 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7724 (mtp180)
REVERT: A  303 LYS cc_start: 0.6873 (tttm) cc_final: 0.6465 (tttp)
REVERT: A  304 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7453 (mmt)
REVERT: A  318 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7883 (tp30)
REVERT: B   18 PHE cc_start: 0.8298 (t80) cc_final: 0.7701 (m-80)
REVERT: B   70 MET cc_start: 0.8781 (mtm) cc_final: 0.8440 (mtp)
REVERT: B  163 GLN cc_start: 0.7682 (mt0) cc_final: 0.7287 (mt0)
REVERT: B  295 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7581 (mtp85)
REVERT: B  303 LYS cc_start: 0.6879 (tttm) cc_final: 0.6474 (tttp)
REVERT: B  304 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7468 (mmt)
  outliers start: 22
  outliers final: 11
  residues processed: 106
  average time/residue: 1.3201
  time to fit residues: 148.4774
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  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  295 ARG
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  295 ARG
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0670
   chunk 89 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 92 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0670
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.3656

-------------------------------------------------------------------------------
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 286 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.120316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.097029 restraints weight = 9736.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.38
r_work: 0.2912 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8532  Z= 0.118
  Angle     :  0.571   7.237  11652  Z= 0.289
  Chirality :  0.042   0.226   1392
  Planarity :  0.005   0.058   1402
  Dihedral  :  9.833  55.249   1322
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.42 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.28), residues: 1050
  helix:  2.34 (0.20), residues: 756
  sheet: -3.51 (0.71), residues: 20
  loop : -2.32 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 410 
 HIS   0.002   0.001   HIS A 497 
 PHE   0.012   0.001   PHE A 351 
 TYR   0.007   0.001   TYR A  40 
 ARG   0.003   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  501)
  hydrogen bonds       : angle       3.55753 ( 1491)
  covalent geometry    : bond        0.00247 ( 8532)
  covalent geometry    : angle       0.57097 (11652)

*********************** 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
  109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8225 (t80) cc_final: 0.7657 (m-80)
REVERT: A   70 MET cc_start: 0.8765 (mtm) cc_final: 0.8431 (mtp)
REVERT: A  163 GLN cc_start: 0.7412 (mt0) cc_final: 0.7155 (mt0)
REVERT: A  303 LYS cc_start: 0.6840 (tttm) cc_final: 0.6442 (tttp)
REVERT: A  304 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7422 (mmt)
REVERT: A  318 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7885 (tp30)
REVERT: B   18 PHE cc_start: 0.8155 (t80) cc_final: 0.7588 (m-80)
REVERT: B   70 MET cc_start: 0.8774 (mtm) cc_final: 0.8440 (mtp)
REVERT: B  163 GLN cc_start: 0.7393 (mt0) cc_final: 0.7134 (mt0)
REVERT: B  256 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6766 (pm20)
REVERT: B  303 LYS cc_start: 0.6848 (tttm) cc_final: 0.6455 (tttp)
REVERT: B  304 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7436 (mmt)
  outliers start: 12
  outliers final: 5
  residues processed: 102
  average time/residue: 1.6281
  time to fit residues: 175.4842
Evaluate side-chains
  103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  156 LEU
Chi-restraints excluded: chain B residue  256 GLN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 57 optimal weight:    0.2980
   chunk 81 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.118094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.094564 restraints weight = 9706.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.36
r_work: 0.2882 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1982

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= 0.129
  Angle     :  0.598   7.743  11652  Z= 0.301
  Chirality :  0.043   0.226   1392
  Planarity :  0.005   0.058   1402
  Dihedral  :  9.806  54.272   1322
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.28), residues: 1050
  helix:  2.37 (0.19), residues: 756
  sheet: -3.46 (0.72), residues: 20
  loop : -2.25 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 410 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.011   0.001   PHE B 528 
 TYR   0.007   0.001   TYR B 500 
 ARG   0.002   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04782 (  501)
  hydrogen bonds       : angle       3.55251 ( 1491)
  covalent geometry    : bond        0.00283 ( 8532)
  covalent geometry    : angle       0.59816 (11652)

*********************** 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
  113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8196 (t80) cc_final: 0.7647 (m-80)
REVERT: A   70 MET cc_start: 0.8770 (mtm) cc_final: 0.8411 (mtp)
REVERT: A  163 GLN cc_start: 0.7423 (mt0) cc_final: 0.7163 (mt0)
REVERT: A  303 LYS cc_start: 0.6851 (tttm) cc_final: 0.6451 (tttp)
REVERT: A  304 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7426 (mmt)
REVERT: A  318 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7882 (tp30)
REVERT: B   18 PHE cc_start: 0.8172 (t80) cc_final: 0.7594 (m-80)
REVERT: B   70 MET cc_start: 0.8770 (mtm) cc_final: 0.8413 (mtp)
REVERT: B  163 GLN cc_start: 0.7422 (mt0) cc_final: 0.7170 (mt0)
REVERT: B  256 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6792 (pm20)
REVERT: B  303 LYS cc_start: 0.6857 (tttm) cc_final: 0.6464 (tttp)
REVERT: B  304 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7437 (mmt)
  outliers start: 13
  outliers final: 7
  residues processed: 106
  average time/residue: 1.5581
  time to fit residues: 174.8494
Evaluate side-chains
  109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
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  156 LEU
Chi-restraints excluded: chain B residue  256 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0370
   chunk 50 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.5258

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.120554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.097212 restraints weight = 9667.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.38
r_work: 0.2917 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8532  Z= 0.117
  Angle     :  0.572   7.187  11652  Z= 0.289
  Chirality :  0.042   0.242   1392
  Planarity :  0.005   0.058   1402
  Dihedral  :  9.516  53.749   1322
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.28), residues: 1050
  helix:  2.55 (0.19), residues: 744
  sheet: -3.42 (0.73), residues: 20
  loop : -2.36 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 410 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.011   0.001   PHE A 351 
 TYR   0.007   0.001   TYR B  40 
 ARG   0.004   0.000   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 (  501)
  hydrogen bonds       : angle       3.49600 ( 1491)
  covalent geometry    : bond        0.00249 ( 8532)
  covalent geometry    : angle       0.57217 (11652)

********************** 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
  118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.8144 (t80) cc_final: 0.7548 (m-80)
REVERT: A   70 MET cc_start: 0.8763 (mtm) cc_final: 0.8433 (mtp)
REVERT: A  163 GLN cc_start: 0.7413 (mt0) cc_final: 0.7174 (mt0)
REVERT: A  303 LYS cc_start: 0.6838 (tttm) cc_final: 0.6443 (tttp)
REVERT: A  304 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7418 (mmt)
REVERT: A  318 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7886 (tp30)
REVERT: B   18 PHE cc_start: 0.8142 (t80) cc_final: 0.7565 (m-80)
REVERT: B   70 MET cc_start: 0.8766 (mtm) cc_final: 0.8435 (mtp)
REVERT: B  163 GLN cc_start: 0.7423 (mt0) cc_final: 0.7192 (mt0)
REVERT: B  256 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6756 (pm20)
REVERT: B  303 LYS cc_start: 0.6838 (tttm) cc_final: 0.6449 (tttp)
REVERT: B  304 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7418 (mmt)
  outliers start: 12
  outliers final: 7
  residues processed: 113
  average time/residue: 1.2849
  time to fit residues: 154.0135
Evaluate side-chains
  109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
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  156 LEU
Chi-restraints excluded: chain B residue  256 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0870
   chunk 13 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 66 optimal weight:    0.3980
   chunk 77 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.2362

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.117132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.093361 restraints weight = 9709.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.39
r_work: 0.2861 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1970

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= 0.147
  Angle     :  0.629   8.046  11652  Z= 0.318
  Chirality :  0.044   0.217   1392
  Planarity :  0.005   0.059   1402
  Dihedral  :  9.764  55.164   1322
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.28), residues: 1050
  helix:  2.33 (0.20), residues: 750
  sheet: -3.41 (0.74), residues: 20
  loop : -2.14 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 410 
 HIS   0.006   0.001   HIS B 160 
 PHE   0.014   0.002   PHE B 568 
 TYR   0.008   0.001   TYR A 500 
 ARG   0.002   0.000   ARG B 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05393 (  501)
  hydrogen bonds       : angle       3.59300 ( 1491)
  covalent geometry    : bond        0.00334 ( 8532)
  covalent geometry    : angle       0.62862 (11652)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6891.91 seconds
wall clock time: 120 minutes 42.47 seconds (7242.47 seconds total)