Starting phenix.real_space_refine
on Wed Mar  4 03:33:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9e_24934/03_2026/7s9e_24934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9e_24934/03_2026/7s9e_24934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s9e_24934/03_2026/7s9e_24934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9e_24934/03_2026/7s9e_24934.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9e_24934/03_2026/7s9e_24934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9e_24934/03_2026/7s9e_24934.cif"
  }
  resolution = 3.7
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6870      2.51       5
     N    1682      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10476
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 677, 5228
          Classifications: {'peptide': 677}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 643}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 5228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 677, 5228
          Classifications: {'peptide': 677}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 643}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'SAL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'SAL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.36, per 1000 atoms: 0.23
  Number of scatterers: 10476
  At special positions: 0
  Unit cell: (117.993, 113.741, 113.741, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1876      8.00
     N    1682      7.00
     C    6870      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: 0.84
  Conformation dependent library (CDL) restraints added in 507.5 milliseconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2500

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      65.9% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 31
    Processing helix  chain 'A' and resid 44 through 48
      removed outlier: 4.077A  pdb=" N   LYS A  47 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 66 through 71
      removed outlier: 4.123A  pdb=" N   TRP A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 66 through 71'
    Processing helix  chain 'A' and resid 78 through 104
      removed outlier: 3.803A  pdb=" N   GLY A  82 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 109 through 127
      removed outlier: 3.951A  pdb=" N   LEU A 113 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 137 through 152
    Processing helix  chain 'A' and resid 168 through 196
    Processing helix  chain 'A' and resid 197 through 204
      removed outlier: 4.180A  pdb=" N   PHE A 200 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 230
      removed outlier: 3.579A  pdb=" N   PHE A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 258 through 282
      removed outlier: 3.888A  pdb=" N   GLU A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 308
      removed outlier: 4.088A  pdb=" N   PHE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 314
    Processing helix  chain 'A' and resid 335 through 338
    Processing helix  chain 'A' and resid 339 through 365
      removed outlier: 3.838A  pdb=" N   LYS A 364 " --> pdb=" O   THR A 360 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   HIS A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 396 through 407
      removed outlier: 3.580A  pdb=" N   SER A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY A 407 " --> pdb=" O   GLN A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
    Processing helix  chain 'A' and resid 436 through 448
      removed outlier: 3.804A  pdb=" N   LEU A 440 " --> pdb=" O   PRO A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 454
    Processing helix  chain 'A' and resid 456 through 465
      removed outlier: 3.763A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 481
    Processing helix  chain 'A' and resid 484 through 502
    Processing helix  chain 'A' and resid 524 through 526
      No H-bonds generated for 'chain 'A' and resid 524 through 526'
    Processing helix  chain 'A' and resid 549 through 560
      removed outlier: 3.501A  pdb=" N   THR A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 680 through 690
      removed outlier: 3.826A  pdb=" N   ASN A 690 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 701
    Processing helix  chain 'A' and resid 705 through 721
    Processing helix  chain 'B' and resid 24 through 31
    Processing helix  chain 'B' and resid 44 through 48
      removed outlier: 4.077A  pdb=" N   LYS B  47 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 64
    Processing helix  chain 'B' and resid 66 through 71
      removed outlier: 4.123A  pdb=" N   TRP B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 66 through 71'
    Processing helix  chain 'B' and resid 78 through 104
      removed outlier: 3.804A  pdb=" N   GLY B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 109 through 127
      removed outlier: 3.951A  pdb=" N   LEU B 113 " --> pdb=" O   PRO B 109 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 137 through 152
    Processing helix  chain 'B' and resid 168 through 196
    Processing helix  chain 'B' and resid 197 through 204
      removed outlier: 4.180A  pdb=" N   PHE B 200 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 230
      removed outlier: 3.578A  pdb=" N   PHE B 230 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 258 through 282
      removed outlier: 3.890A  pdb=" N   GLU B 280 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 308
      removed outlier: 4.088A  pdb=" N   PHE B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 314
    Processing helix  chain 'B' and resid 335 through 338
    Processing helix  chain 'B' and resid 339 through 365
      removed outlier: 3.837A  pdb=" N   LYS B 364 " --> pdb=" O   THR B 360 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   HIS B 365 " --> pdb=" O   LEU B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 396 through 407
      removed outlier: 3.580A  pdb=" N   SER B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY B 407 " --> pdb=" O   GLN B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
    Processing helix  chain 'B' and resid 436 through 448
      removed outlier: 3.805A  pdb=" N   LEU B 440 " --> pdb=" O   PRO B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 454
    Processing helix  chain 'B' and resid 456 through 465
      removed outlier: 3.763A  pdb=" N   PHE B 460 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 481
    Processing helix  chain 'B' and resid 484 through 502
    Processing helix  chain 'B' and resid 524 through 526
      No H-bonds generated for 'chain 'B' and resid 524 through 526'
    Processing helix  chain 'B' and resid 549 through 560
      removed outlier: 3.501A  pdb=" N   THR B 560 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 579
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 680 through 690
      removed outlier: 3.827A  pdb=" N   ASN B 690 " --> pdb=" O   ASP B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 697 through 701
    Processing helix  chain 'B' and resid 705 through 721
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
      removed outlier: 4.475A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   GLN A 513 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 11.934A  pdb=" N   ILE A 535 " --> pdb=" O   GLN A 513 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ILE A 642 " --> pdb=" O   TYR A 675 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ALA A 677 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU A 644 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135
    Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522
      removed outlier: 4.475A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.380A  pdb=" N   GLN B 513 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 11.934A  pdb=" N   ILE B 535 " --> pdb=" O   GLN B 513 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ILE B 642 " --> pdb=" O   TYR B 675 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ALA B 677 " --> pdb=" O   ILE B 642 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU B 644 " --> pdb=" O   ALA B 677 " (cutoff:3.500A)

    622 hydrogen bonds defined for protein.
    1806 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: 1.66

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3176
        1.34 -     1.46: 2107
        1.46 -     1.58: 5351
        1.58 -     1.70: 0
        1.70 -     1.83: 78
  Bond restraints: 10712
  Sorted by residual:
  bond pdb=" N   VAL B  27 "
       pdb=" CA  VAL B  27 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.20e-02 6.94e+03 9.18e+00
  bond pdb=" N   ILE B  22 "
       pdb=" CA  ILE B  22 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.29e-02 6.01e+03 8.87e+00
  bond pdb=" N   ILE A 494 "
       pdb=" CA  ILE A 494 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.70e+00
  bond pdb=" N   ILE A  22 "
       pdb=" CA  ILE A  22 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.29e-02 6.01e+03 8.54e+00
  bond pdb=" N   ILE B 494 "
       pdb=" CA  ILE B 494 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.21e-02 6.83e+03 8.38e+00
  ... (remaining 10707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 14117
        1.85 -     3.69: 363
        3.69 -     5.54: 66
        5.54 -     7.38: 12
        7.38 -     9.23: 2
  Bond angle restraints: 14560
  Sorted by residual:
  angle pdb=" C   GLU B 694 "
        pdb=" N   ASN B 695 "
        pdb=" CA  ASN B 695 "
      ideal   model   delta    sigma   weight residual
     122.83  127.56   -4.73 1.08e+00 8.57e-01 1.92e+01
  angle pdb=" C   GLU A 694 "
        pdb=" N   ASN A 695 "
        pdb=" CA  ASN A 695 "
      ideal   model   delta    sigma   weight residual
     122.83  127.56   -4.73 1.08e+00 8.57e-01 1.91e+01
  angle pdb=" CA  SER B  24 "
        pdb=" C   SER B  24 "
        pdb=" O   SER B  24 "
      ideal   model   delta    sigma   weight residual
     121.87  117.24    4.63 1.16e+00 7.43e-01 1.59e+01
  angle pdb=" N   SER A  24 "
        pdb=" CA  SER A  24 "
        pdb=" C   SER A  24 "
      ideal   model   delta    sigma   weight residual
     110.53  105.46    5.07 1.29e+00 6.01e-01 1.54e+01
  angle pdb=" CA  SER A  24 "
        pdb=" C   SER A  24 "
        pdb=" O   SER A  24 "
      ideal   model   delta    sigma   weight residual
     121.94  117.49    4.45 1.15e+00 7.56e-01 1.50e+01
  ... (remaining 14555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 5760
       17.92 -    35.85: 482
       35.85 -    53.77: 80
       53.77 -    71.69: 4
       71.69 -    89.62: 8
  Dihedral angle restraints: 6334
    sinusoidal: 2428
      harmonic: 3906
  Sorted by residual:
  dihedral pdb=" CA  ASN B 695 "
           pdb=" C   ASN B 695 "
           pdb=" N   PRO B 696 "
           pdb=" CA  PRO B 696 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.89   25.11     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  ASN A 695 "
           pdb=" C   ASN A 695 "
           pdb=" N   PRO A 696 "
           pdb=" CA  PRO A 696 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.93   25.07     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  VAL B 268 "
           pdb=" C   VAL B 268 "
           pdb=" N   PHE B 269 "
           pdb=" CA  PHE B 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.22   21.78     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 6331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1145
       0.040 -    0.080: 392
       0.080 -    0.120: 167
       0.120 -    0.160: 17
       0.160 -    0.200: 5
  Chirality restraints: 1726
  Sorted by residual:
  chirality pdb=" CB  THR B 128 "
            pdb=" CA  THR B 128 "
            pdb=" OG1 THR B 128 "
            pdb=" CG2 THR B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CB  THR A 128 "
            pdb=" CA  THR A 128 "
            pdb=" OG1 THR A 128 "
            pdb=" CG2 THR A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CA  VAL A  27 "
            pdb=" N   VAL A  27 "
            pdb=" C   VAL A  27 "
            pdb=" CB  VAL A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 1723 not shown)

  Planarity restraints: 1816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 288 "    0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO A 289 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 288 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO B 289 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 289 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 289 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A  21 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   PRO A  21 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PRO A  21 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A  22 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1813 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 990
        2.74 -     3.28: 11442
        3.28 -     3.82: 17388
        3.82 -     4.36: 20002
        4.36 -     4.90: 34045
  Nonbonded interactions: 83867
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 167 "
            pdb=" OE1 GLU B 169 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER A 167 "
            pdb=" OE1 GLU A 169 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER B  41 "
            pdb=" O   ASP B  44 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OG  SER A  41 "
            pdb=" O   ASP A  44 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   PHE B 101 "
            pdb=" OG  SER B 141 "
     model   vdw
     2.225 3.040
  ... (remaining 83862 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.790
  Find NCS groups from input model:        0.080
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
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      :  0.004   0.038  10712  Z= 0.205
  Angle     :  0.721   9.226  14560  Z= 0.411
  Chirality :  0.047   0.200   1726
  Planarity :  0.004   0.045   1816
  Dihedral  : 13.528  89.618   3834
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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 are not related in a simple way.
  whole: -0.36 (0.23), residues: 1346
  helix:  0.73 (0.18), residues: 838
  sheet:  1.28 (0.94), residues: 36
  loop : -2.17 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 716 
 TYR   0.012   0.001   TYR A  16 
 PHE   0.021   0.002   PHE B 198 
 TRP   0.013   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10712)
  covalent geometry    : angle       0.72119 (14560)
  hydrogen bonds       : bond        0.12910 (  622)
  hydrogen bonds       : angle       5.75772 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.8118 (m-10) cc_final: 0.7696 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0889
  time to fit residues: 19.5314
Evaluate side-chains
  111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0570
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    1.1500

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

Flipped N/Q/H residues before XYZ refinement:
A 131 HIS
A 256 ASN
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 HIS
B 256 ASN
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.124707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.095528 restraints weight = 17431.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.094379 restraints weight = 13510.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.095458 restraints weight = 10865.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.095760 restraints weight = 9824.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.095777 restraints weight = 8850.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10712  Z= 0.159
  Angle     :  0.620   5.831  14560  Z= 0.319
  Chirality :  0.045   0.154   1726
  Planarity :  0.004   0.049   1816
  Dihedral  :  5.144  51.103   1450
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  7.14 %
    Favored  : 91.29 %
  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 are not related in a simple way.
  whole: -0.05 (0.23), residues: 1346
  helix:  0.98 (0.18), residues: 844
  sheet:  1.52 (0.95), residues: 36
  loop : -2.10 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 572 
 TYR   0.016   0.001   TYR A 228 
 PHE   0.017   0.001   PHE B 111 
 TRP   0.009   0.001   TRP B 472 
 HIS   0.005   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10712)
  covalent geometry    : angle       0.61955 (14560)
  hydrogen bonds       : bond        0.05115 (  622)
  hydrogen bonds       : angle       4.66921 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: B  326 LEU cc_start: 0.8423 (mt) cc_final: 0.8007 (mt)
  outliers start: 18
  outliers final: 14
  residues processed: 130
  average time/residue: 0.0891
  time to fit residues: 17.4434
Evaluate side-chains
  127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 118 optimal weight:    0.0040
   chunk 133 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0470
   chunk 124 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.8092

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 GLN
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.126202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.095494 restraints weight = 17341.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.096738 restraints weight = 13155.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.097137 restraints weight = 10541.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097441 restraints weight = 8300.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.097596 restraints weight = 8007.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10712  Z= 0.131
  Angle     :  0.565   5.226  14560  Z= 0.290
  Chirality :  0.044   0.150   1726
  Planarity :  0.004   0.046   1816
  Dihedral  :  4.948  47.271   1450
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.93 %
    Favored  : 88.24 %
  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 are not related in a simple way.
  whole:  0.32 (0.24), residues: 1346
  helix:  1.28 (0.18), residues: 844
  sheet:  1.69 (0.98), residues: 36
  loop : -1.98 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 631 
 TYR   0.015   0.001   TYR B 578 
 PHE   0.014   0.001   PHE A 111 
 TRP   0.007   0.001   TRP B 472 
 HIS   0.002   0.001   HIS B  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10712)
  covalent geometry    : angle       0.56506 (14560)
  hydrogen bonds       : bond        0.04442 (  622)
  hydrogen bonds       : angle       4.32322 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 MET cc_start: 0.8352 (mmm) cc_final: 0.7703 (mmm)
REVERT: A  527 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6989 (pm20)
REVERT: B  225 MET cc_start: 0.8347 (mmm) cc_final: 0.7741 (mmm)
REVERT: B  326 LEU cc_start: 0.8396 (mt) cc_final: 0.7969 (mt)
REVERT: B  527 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7315 (pt0)
  outliers start: 21
  outliers final: 15
  residues processed: 142
  average time/residue: 0.0849
  time to fit residues: 18.3618
Evaluate side-chains
  133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 127 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 3 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.125509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.094848 restraints weight = 17423.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.096408 restraints weight = 16369.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.097168 restraints weight = 11381.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.097268 restraints weight = 8818.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.097459 restraints weight = 8231.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10712  Z= 0.146
  Angle     :  0.583   9.304  14560  Z= 0.293
  Chirality :  0.044   0.151   1726
  Planarity :  0.004   0.047   1816
  Dihedral  :  4.865  46.148   1450
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.46 %
    Favored  : 85.19 %
  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 are not related in a simple way.
  whole:  0.46 (0.24), residues: 1346
  helix:  1.38 (0.18), residues: 846
  sheet:  1.69 (0.98), residues: 36
  loop : -1.91 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 399 
 TYR   0.012   0.001   TYR A  16 
 PHE   0.015   0.001   PHE A 111 
 TRP   0.007   0.001   TRP B 472 
 HIS   0.002   0.001   HIS B 707 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10712)
  covalent geometry    : angle       0.58291 (14560)
  hydrogen bonds       : bond        0.04334 (  622)
  hydrogen bonds       : angle       4.22789 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7696 (mppt)
REVERT: A  225 MET cc_start: 0.8395 (mmm) cc_final: 0.7667 (mmm)
REVERT: A  527 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7266 (pt0)
REVERT: B  225 MET cc_start: 0.8401 (mmm) cc_final: 0.7681 (mmm)
REVERT: B  326 LEU cc_start: 0.8337 (mt) cc_final: 0.7919 (mt)
  outliers start: 27
  outliers final: 20
  residues processed: 138
  average time/residue: 0.0822
  time to fit residues: 17.4837
Evaluate side-chains
  134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 128 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 127 optimal weight:    0.0470
   chunk 123 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   overall best weight:    2.0084

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.123457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.093465 restraints weight = 17407.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.092564 restraints weight = 13488.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.093501 restraints weight = 11517.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.093805 restraints weight = 9772.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.093976 restraints weight = 8617.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10712  Z= 0.195
  Angle     :  0.619   8.095  14560  Z= 0.315
  Chirality :  0.045   0.151   1726
  Planarity :  0.004   0.045   1816
  Dihedral  :  4.949  46.699   1450
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 12.54 %
    Favored  : 84.15 %
  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 are not related in a simple way.
  whole:  0.40 (0.24), residues: 1346
  helix:  1.32 (0.18), residues: 846
  sheet:  1.61 (0.97), residues: 36
  loop : -1.90 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 399 
 TYR   0.019   0.002   TYR A 546 
 PHE   0.016   0.002   PHE A 111 
 TRP   0.007   0.001   TRP A 472 
 HIS   0.003   0.001   HIS B 707 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (10712)
  covalent geometry    : angle       0.61900 (14560)
  hydrogen bonds       : bond        0.04566 (  622)
  hydrogen bonds       : angle       4.25502 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7662 (mppt)
REVERT: A  225 MET cc_start: 0.8351 (mmm) cc_final: 0.7666 (mmm)
REVERT: A  527 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7334 (pt0)
REVERT: B   55 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7658 (mppt)
REVERT: B  225 MET cc_start: 0.8351 (mmm) cc_final: 0.7674 (mmm)
REVERT: B  326 LEU cc_start: 0.8366 (mt) cc_final: 0.7942 (mt)
  outliers start: 38
  outliers final: 24
  residues processed: 145
  average time/residue: 0.0809
  time to fit residues: 17.9198
Evaluate side-chains
  141 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   70 TRP
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue   70 TRP
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 97 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0470
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 56 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A 253 ASN
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 ASN
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.126742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.096199 restraints weight = 17523.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097584 restraints weight = 15346.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.098367 restraints weight = 10939.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.098475 restraints weight = 8825.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.098606 restraints weight = 8205.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10712  Z= 0.119
  Angle     :  0.559   6.726  14560  Z= 0.282
  Chirality :  0.044   0.160   1726
  Planarity :  0.004   0.046   1816
  Dihedral  :  4.775  43.792   1450
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.55 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.24), residues: 1346
  helix:  1.53 (0.18), residues: 848
  sheet:  1.75 (0.99), residues: 36
  loop : -1.85 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 399 
 TYR   0.011   0.001   TYR A  16 
 PHE   0.012   0.001   PHE A 111 
 TRP   0.009   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10712)
  covalent geometry    : angle       0.55881 (14560)
  hydrogen bonds       : bond        0.04107 (  622)
  hydrogen bonds       : angle       4.11350 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7679 (mppt)
REVERT: A  225 MET cc_start: 0.8410 (mmm) cc_final: 0.7603 (mmm)
REVERT: A  527 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7202 (pt0)
REVERT: B   55 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7663 (mppt)
REVERT: B  225 MET cc_start: 0.8413 (mmm) cc_final: 0.7611 (mmm)
REVERT: B  326 LEU cc_start: 0.8306 (mt) cc_final: 0.7894 (mt)
  outliers start: 30
  outliers final: 26
  residues processed: 153
  average time/residue: 0.0773
  time to fit residues: 18.2189
Evaluate side-chains
  145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue   64 PHE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Chi-restraints excluded: chain B residue  620 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 127 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0030
   chunk 11 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 105 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    2.1998

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.122916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.091786 restraints weight = 17405.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.094760 restraints weight = 15778.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.095033 restraints weight = 9534.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.094631 restraints weight = 7982.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.094760 restraints weight = 8622.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10712  Z= 0.209
  Angle     :  0.650   6.821  14560  Z= 0.327
  Chirality :  0.046   0.159   1726
  Planarity :  0.004   0.046   1816
  Dihedral  :  4.913  44.993   1450
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.03 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.24), residues: 1346
  helix:  1.39 (0.18), residues: 848
  sheet:  1.59 (0.99), residues: 36
  loop : -1.90 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 399 
 TYR   0.016   0.002   TYR A 578 
 PHE   0.016   0.002   PHE A 111 
 TRP   0.006   0.001   TRP A 472 
 HIS   0.004   0.001   HIS A 707 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (10712)
  covalent geometry    : angle       0.64994 (14560)
  hydrogen bonds       : bond        0.04590 (  622)
  hydrogen bonds       : angle       4.24289 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7683 (mppt)
REVERT: A  497 MET cc_start: 0.7940 (mmp) cc_final: 0.7726 (mmp)
REVERT: B   55 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7685 (mppt)
REVERT: B  326 LEU cc_start: 0.8403 (mt) cc_final: 0.8007 (mt)
  outliers start: 36
  outliers final: 35
  residues processed: 136
  average time/residue: 0.0881
  time to fit residues: 18.2404
Evaluate side-chains
  147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   70 TRP
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue   64 PHE
Chi-restraints excluded: chain B residue   70 TRP
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  620 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 93 optimal weight:    0.0470
   chunk 117 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 110 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0470
   chunk 57 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.126828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.098537 restraints weight = 17384.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097357 restraints weight = 13040.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.098584 restraints weight = 11218.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.098711 restraints weight = 9220.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.099093 restraints weight = 8214.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10712  Z= 0.120
  Angle     :  0.573   7.219  14560  Z= 0.284
  Chirality :  0.043   0.156   1726
  Planarity :  0.004   0.045   1816
  Dihedral  :  4.748  41.820   1450
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.72 %
    Favored  : 80.40 %
  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 are not related in a simple way.
  whole:  0.72 (0.24), residues: 1346
  helix:  1.66 (0.19), residues: 840
  sheet:  1.76 (1.01), residues: 36
  loop : -1.90 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 399 
 TYR   0.009   0.001   TYR A  16 
 PHE   0.011   0.001   PHE A 111 
 TRP   0.009   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10712)
  covalent geometry    : angle       0.57290 (14560)
  hydrogen bonds       : bond        0.04009 (  622)
  hydrogen bonds       : angle       4.07196 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7644 (mppt)
REVERT: A  225 MET cc_start: 0.8475 (mmm) cc_final: 0.7986 (mmm)
REVERT: A  262 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7718 (mt)
REVERT: A  527 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7121 (pt0)
REVERT: B   55 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7655 (mppt)
REVERT: B  225 MET cc_start: 0.8447 (mmm) cc_final: 0.7924 (mmm)
REVERT: B  262 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7727 (mt)
REVERT: B  326 LEU cc_start: 0.8336 (mt) cc_final: 0.7984 (mt)
REVERT: B  527 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7165 (pt0)
  outliers start: 33
  outliers final: 26
  residues processed: 139
  average time/residue: 0.0831
  time to fit residues: 17.8288
Evaluate side-chains
  145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue   64 PHE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0570
   chunk 43 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.1702

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.125279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.096707 restraints weight = 17480.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.095585 restraints weight = 13131.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.096643 restraints weight = 11494.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.096806 restraints weight = 9511.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.096909 restraints weight = 8443.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10712  Z= 0.143
  Angle     :  0.588   7.646  14560  Z= 0.291
  Chirality :  0.044   0.161   1726
  Planarity :  0.004   0.046   1816
  Dihedral  :  4.712  41.568   1450
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.42 %
    Favored  : 79.62 %
  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 are not related in a simple way.
  whole:  0.85 (0.24), residues: 1346
  helix:  1.76 (0.19), residues: 834
  sheet:  1.70 (0.98), residues: 36
  loop : -1.79 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 399 
 TYR   0.019   0.001   TYR B 578 
 PHE   0.013   0.001   PHE A 111 
 TRP   0.007   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 707 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10712)
  covalent geometry    : angle       0.58798 (14560)
  hydrogen bonds       : bond        0.04128 (  622)
  hydrogen bonds       : angle       4.06550 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7644 (mppt)
REVERT: A  225 MET cc_start: 0.8406 (mmm) cc_final: 0.7761 (mmm)
REVERT: A  262 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7738 (mt)
REVERT: A  497 MET cc_start: 0.7715 (mmp) cc_final: 0.7175 (mmm)
REVERT: B   55 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7661 (mppt)
REVERT: B  225 MET cc_start: 0.8403 (mmm) cc_final: 0.7762 (mmm)
REVERT: B  262 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7750 (mt)
REVERT: B  326 LEU cc_start: 0.8369 (mt) cc_final: 0.8010 (mt)
REVERT: B  497 MET cc_start: 0.7689 (mmp) cc_final: 0.7138 (mmm)
  outliers start: 34
  outliers final: 31
  residues processed: 129
  average time/residue: 0.0863
  time to fit residues: 16.9608
Evaluate side-chains
  143 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   70 TRP
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue   64 PHE
Chi-restraints excluded: chain B residue   70 TRP
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0770
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 109 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 121 optimal weight:    0.4980
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.127097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.098406 restraints weight = 17257.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.097569 restraints weight = 13703.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.098711 restraints weight = 11303.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.098910 restraints weight = 9360.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.099134 restraints weight = 8422.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10712  Z= 0.120
  Angle     :  0.566   8.323  14560  Z= 0.280
  Chirality :  0.043   0.162   1726
  Planarity :  0.004   0.045   1816
  Dihedral  :  4.652  40.009   1450
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.94 %
    Favored  : 79.53 %
  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 are not related in a simple way.
  whole:  0.90 (0.24), residues: 1346
  helix:  1.80 (0.19), residues: 838
  sheet:  1.63 (0.98), residues: 36
  loop : -1.81 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 399 
 TYR   0.009   0.001   TYR A  16 
 PHE   0.012   0.001   PHE A 111 
 TRP   0.008   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10712)
  covalent geometry    : angle       0.56593 (14560)
  hydrogen bonds       : bond        0.03933 (  622)
  hydrogen bonds       : angle       4.00857 ( 1806)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7650 (mppt)
REVERT: A  225 MET cc_start: 0.8428 (mmm) cc_final: 0.7769 (mmm)
REVERT: A  262 LEU cc_start: 0.8184 (mm) cc_final: 0.7912 (mt)
REVERT: A  497 MET cc_start: 0.7607 (mmp) cc_final: 0.7015 (mmm)
REVERT: B   55 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7654 (mppt)
REVERT: B  225 MET cc_start: 0.8420 (mmm) cc_final: 0.7768 (mmm)
REVERT: B  262 LEU cc_start: 0.8174 (mm) cc_final: 0.7906 (mt)
REVERT: B  326 LEU cc_start: 0.8349 (mt) cc_final: 0.8026 (mt)
REVERT: B  497 MET cc_start: 0.7618 (mmp) cc_final: 0.7030 (mmm)
  outliers start: 29
  outliers final: 29
  residues processed: 137
  average time/residue: 0.0804
  time to fit residues: 16.9965
Evaluate side-chains
  139 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   63 MET
Chi-restraints excluded: chain B residue   64 PHE
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  527 GLU
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 129 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 115 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0870
   chunk 6 optimal weight:    0.2980
   chunk 127 optimal weight:    0.4980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 650 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.127703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.099015 restraints weight = 17535.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.098155 restraints weight = 13979.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.099401 restraints weight = 11320.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.099749 restraints weight = 9285.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.099873 restraints weight = 8693.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10712  Z= 0.116
  Angle     :  0.569   8.946  14560  Z= 0.281
  Chirality :  0.043   0.165   1726
  Planarity :  0.004   0.047   1816
  Dihedral  :  4.606  39.218   1450
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.86 %
    Favored  : 79.53 %
  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 are not related in a simple way.
  whole:  0.98 (0.24), residues: 1346
  helix:  1.88 (0.19), residues: 832
  sheet:  1.60 (0.97), residues: 36
  loop : -1.73 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 399 
 TYR   0.009   0.001   TYR A  16 
 PHE   0.011   0.001   PHE A 111 
 TRP   0.008   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10712)
  covalent geometry    : angle       0.56900 (14560)
  hydrogen bonds       : bond        0.03992 (  622)
  hydrogen bonds       : angle       3.98877 ( 1806)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1492.27 seconds
wall clock time: 26 minutes 43.50 seconds (1603.50 seconds total)