Starting phenix.real_space_refine
on Fri Feb 14 18:56:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9e_24934/02_2025/7s9e_24934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9e_24934/02_2025/7s9e_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_24934/02_2025/7s9e_24934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9e_24934/02_2025/7s9e_24934.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9e_24934/02_2025/7s9e_24934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9e_24934/02_2025/7s9e_24934.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.10, per 1000 atoms: 0.58
  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: 2.58
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.98
  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: 3.28

  Time building geometry restraints manager: 3.00 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: 0.05
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:             0.890
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.040
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.710
-------------------------------------------------------------------------------
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= 0.240
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (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
 TRP   0.013   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B  25 
 PHE   0.021   0.002   PHE B 198 
 TYR   0.012   0.001   TYR A  16 
 ARG   0.007   0.001   ARG B 716 

*********************** 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  : 1.085 
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: 0.2090
  time to fit residues: 45.1862
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  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 121 optimal weight:    0.6980
   overall best weight:    2.3388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.121995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.091794 restraints weight = 17265.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.093020 restraints weight = 15508.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.093823 restraints weight = 12279.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10712  Z= 0.336
  Angle     :  0.668   6.072  14560  Z= 0.345
  Chirality :  0.047   0.158   1726
  Planarity :  0.005   0.048   1816
  Dihedral  :  5.289  52.702   1450
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  7.67 %
    Favored  : 90.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.23), residues: 1346
  helix:  0.81 (0.18), residues: 848
  sheet:  1.62 (0.96), residues: 36
  loop : -2.11 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 472 
 HIS   0.006   0.001   HIS A 131 
 PHE   0.019   0.002   PHE B 111 
 TYR   0.015   0.002   TYR A  16 
 ARG   0.003   0.000   ARG A 572 

*********************** 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
  138 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
REVERT: B  326 LEU cc_start: 0.8460 (mt) cc_final: 0.8034 (mt)
  outliers start: 19
  outliers final: 15
  residues processed: 127
  average time/residue: 0.2074
  time to fit residues: 38.9926
Evaluate side-chains
  124 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 133 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 365 HIS
** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 548 ASN
B 365 HIS
** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.125351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.094310 restraints weight = 17308.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.095063 restraints weight = 13591.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.095596 restraints weight = 10888.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1398

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= 0.194
  Angle     :  0.575   5.245  14560  Z= 0.297
  Chirality :  0.044   0.146   1726
  Planarity :  0.004   0.045   1816
  Dihedral  :  5.042  49.026   1450
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.06 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.24), residues: 1346
  helix:  1.13 (0.18), residues: 848
  sheet:  1.80 (0.99), residues: 36
  loop : -2.01 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 472 
 HIS   0.003   0.001   HIS B  33 
 PHE   0.014   0.001   PHE A 111 
 TYR   0.015   0.001   TYR B 578 
 ARG   0.002   0.000   ARG B 631 

*********************** 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
  156 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
REVERT: B  326 LEU cc_start: 0.8407 (mt) cc_final: 0.7993 (mt)
  outliers start: 24
  outliers final: 15
  residues processed: 141
  average time/residue: 0.1972
  time to fit residues: 42.0458
Evaluate side-chains
  132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 MET
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 129 optimal weight:    4.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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**
** B 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 = 0.3510 r_free = 0.3510 target = 0.122154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.092058 restraints weight = 17475.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.091647 restraints weight = 13277.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.092711 restraints weight = 12342.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10712  Z= 0.334
  Angle     :  0.649  10.033  14560  Z= 0.330
  Chirality :  0.046   0.153   1726
  Planarity :  0.004   0.046   1816
  Dihedral  :  5.122  49.450   1450
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 12.46 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.23), residues: 1346
  helix:  1.07 (0.18), residues: 848
  sheet:  1.63 (0.98), residues: 36
  loop : -2.01 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B 707 
 PHE   0.017   0.002   PHE B 111 
 TYR   0.016   0.002   TYR A  16 
 ARG   0.002   0.000   ARG A 502 

*********************** 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
  152 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 117
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7690 (mppt)
REVERT: A  206 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8497 (m)
REVERT: A  225 MET cc_start: 0.8322 (mmm) cc_final: 0.8083 (mmm)
REVERT: A  577 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7788 (tmtt)
REVERT: B   55 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7679 (mppt)
REVERT: B  206 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8507 (m)
REVERT: B  225 MET cc_start: 0.8328 (mmm) cc_final: 0.8117 (mmm)
REVERT: B  326 LEU cc_start: 0.8434 (mt) cc_final: 0.8004 (mt)
  outliers start: 35
  outliers final: 24
  residues processed: 140
  average time/residue: 0.2200
  time to fit residues: 45.2869
Evaluate side-chains
  142 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
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  206 THR
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  498 THR
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  196 CYS
Chi-restraints excluded: chain B residue  206 THR
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  498 THR
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 83 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   chunk 114 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   chunk 127 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 106 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 454 GLN ** 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 = 0.3554 r_free = 0.3554 target = 0.125325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.096422 restraints weight = 17349.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.094824 restraints weight = 13663.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.096234 restraints weight = 11515.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10712  Z= 0.179
  Angle     :  0.567   7.699  14560  Z= 0.289
  Chirality :  0.044   0.153   1726
  Planarity :  0.004   0.045   1816
  Dihedral  :  4.930  46.056   1450
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.50 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.24), residues: 1346
  helix:  1.37 (0.18), residues: 848
  sheet:  1.82 (0.99), residues: 36
  loop : -1.96 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 337 
 PHE   0.013   0.001   PHE A 111 
 TYR   0.016   0.001   TYR B 578 
 ARG   0.002   0.000   ARG B 399 

*********************** 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
  162 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 122
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7635 (mppt)
REVERT: A  225 MET cc_start: 0.8353 (mmm) cc_final: 0.7413 (mmm)
REVERT: B   55 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7629 (mppt)
REVERT: B  225 MET cc_start: 0.8381 (mmm) cc_final: 0.7437 (mmm)
REVERT: B  326 LEU cc_start: 0.8365 (mt) cc_final: 0.7944 (mt)
  outliers start: 40
  outliers final: 26
  residues processed: 149
  average time/residue: 0.2124
  time to fit residues: 46.6794
Evaluate side-chains
  140 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
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  266 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  498 THR
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   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  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  498 THR
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  620 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 58 optimal weight:    0.4980
   chunk 114 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 ** 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 = 0.3565 r_free = 0.3565 target = 0.126364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.097175 restraints weight = 17481.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.096033 restraints weight = 13219.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097348 restraints weight = 11408.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10712  Z= 0.186
  Angle     :  0.591  12.733  14560  Z= 0.294
  Chirality :  0.044   0.158   1726
  Planarity :  0.004   0.047   1816
  Dihedral  :  4.800  43.568   1450
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.37 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.24), residues: 1346
  helix:  1.50 (0.18), residues: 846
  sheet:  1.76 (1.00), residues: 36
  loop : -1.88 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 337 
 PHE   0.013   0.001   PHE A 111 
 TYR   0.010   0.001   TYR A  16 
 ARG   0.002   0.000   ARG B 399 

*********************** 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
  158 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7870 (mmmt) cc_final: 0.7608 (mppt)
REVERT: A  225 MET cc_start: 0.8451 (mmm) cc_final: 0.7688 (mmm)
REVERT: A  497 MET cc_start: 0.7486 (mmp) cc_final: 0.6456 (tpt)
REVERT: B   55 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7628 (mppt)
REVERT: B  225 MET cc_start: 0.8425 (mmm) cc_final: 0.7688 (mmm)
REVERT: B  326 LEU cc_start: 0.8324 (mt) cc_final: 0.7917 (mt)
REVERT: B  497 MET cc_start: 0.7621 (mmp) cc_final: 0.6885 (mmm)
  outliers start: 31
  outliers final: 29
  residues processed: 146
  average time/residue: 0.1883
  time to fit residues: 42.1288
Evaluate side-chains
  147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
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  196 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  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  196 CYS
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  423 LEU
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0070
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0020
   chunk 27 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 126 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.3806

-------------------------------------------------------------------------------
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 454 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.128524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.099690 restraints weight = 17601.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.098828 restraints weight = 12552.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.099537 restraints weight = 11260.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10712  Z= 0.165
  Angle     :  0.567   9.847  14560  Z= 0.283
  Chirality :  0.043   0.150   1726
  Planarity :  0.004   0.046   1816
  Dihedral  :  4.648  40.668   1450
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.72 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.24), residues: 1346
  helix:  1.59 (0.18), residues: 852
  sheet:  1.78 (1.02), residues: 36
  loop : -1.82 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 472 
 HIS   0.002   0.000   HIS A 337 
 PHE   0.011   0.001   PHE A 111 
 TYR   0.019   0.001   TYR B 578 
 ARG   0.002   0.000   ARG A 399 

*********************** 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
  158 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7619 (mppt)
REVERT: A  225 MET cc_start: 0.8392 (mmm) cc_final: 0.7602 (mmm)
REVERT: A  497 MET cc_start: 0.7489 (mmp) cc_final: 0.6845 (mmm)
REVERT: B   55 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7647 (mppt)
REVERT: B  225 MET cc_start: 0.8383 (mmm) cc_final: 0.7614 (mmm)
REVERT: B  326 LEU cc_start: 0.8323 (mt) cc_final: 0.8005 (mt)
REVERT: B  497 MET cc_start: 0.7327 (mmp) cc_final: 0.6801 (mmm)
  outliers start: 30
  outliers final: 27
  residues processed: 147
  average time/residue: 0.1981
  time to fit residues: 44.1611
Evaluate side-chains
  142 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
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  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  423 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  624 THR
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  532 VAL
Chi-restraints excluded: chain B residue  624 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3540 r_free = 0.3540 target = 0.124650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.094918 restraints weight = 17485.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.094385 restraints weight = 16400.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.095866 restraints weight = 11816.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10712  Z= 0.279
  Angle     :  0.628  10.032  14560  Z= 0.315
  Chirality :  0.045   0.180   1726
  Planarity :  0.004   0.047   1816
  Dihedral  :  4.750  42.283   1450
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 16.90 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.24), residues: 1346
  helix:  1.57 (0.18), residues: 846
  sheet:  1.79 (0.99), residues: 36
  loop : -1.82 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 472 
 HIS   0.003   0.001   HIS B 707 
 PHE   0.015   0.001   PHE A 111 
 TYR   0.016   0.001   TYR B 546 
 ARG   0.003   0.000   ARG A 399 

*********************** 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
  152 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 115
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7657 (mppt)
REVERT: B   55 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7672 (mppt)
REVERT: B  326 LEU cc_start: 0.8374 (mt) cc_final: 0.8021 (mt)
  outliers start: 37
  outliers final: 34
  residues processed: 136
  average time/residue: 0.2017
  time to fit residues: 42.2719
Evaluate side-chains
  146 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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  195 VAL
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  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  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  410 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  620 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 58 optimal weight:    0.0980
   chunk 68 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 89 optimal weight:    0.2980
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.126345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.096699 restraints weight = 17565.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.096760 restraints weight = 14376.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097598 restraints weight = 11795.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10712  Z= 0.210
  Angle     :  0.598   9.834  14560  Z= 0.297
  Chirality :  0.044   0.169   1726
  Planarity :  0.004   0.046   1816
  Dihedral  :  4.716  41.321   1450
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.24), residues: 1346
  helix:  1.64 (0.18), residues: 846
  sheet:  1.79 (0.98), residues: 36
  loop : -1.79 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  70 
 HIS   0.002   0.001   HIS A 337 
 PHE   0.012   0.001   PHE A 111 
 TYR   0.011   0.001   TYR B 546 
 ARG   0.002   0.000   ARG A 399 

*********************** 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
  153 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7638 (mppt)
REVERT: A  225 MET cc_start: 0.8338 (mmm) cc_final: 0.7381 (mmm)
REVERT: B   55 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7651 (mppt)
REVERT: B  225 MET cc_start: 0.8372 (mmm) cc_final: 0.7433 (mmm)
REVERT: B  326 LEU cc_start: 0.8379 (mt) cc_final: 0.8026 (mt)
  outliers start: 35
  outliers final: 30
  residues processed: 138
  average time/residue: 0.1818
  time to fit residues: 38.4937
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  : 1.059 
-------------------------------------------------------------------------------
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  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  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  192 CYS
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  532 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 123 optimal weight:   10.0000
   chunk 68 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   chunk 121 optimal weight:    0.2980
   chunk 66 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 128 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3546 r_free = 0.3546 target = 0.125015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.095353 restraints weight = 17598.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.095076 restraints weight = 14349.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.095957 restraints weight = 12023.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10712  Z= 0.254
  Angle     :  0.625  10.840  14560  Z= 0.310
  Chirality :  0.044   0.163   1726
  Planarity :  0.004   0.048   1816
  Dihedral  :  4.749  41.531   1450
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.77 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.24), residues: 1346
  helix:  1.61 (0.18), residues: 846
  sheet:  1.65 (0.97), residues: 36
  loop : -1.76 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  70 
 HIS   0.002   0.001   HIS B 707 
 PHE   0.014   0.001   PHE A 111 
 TYR   0.014   0.001   TYR B 546 
 ARG   0.002   0.000   ARG A 399 

********************** 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
  148 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7635 (mppt)
REVERT: A  225 MET cc_start: 0.8339 (mmm) cc_final: 0.7371 (mmm)
REVERT: A  316 ASP cc_start: 0.8300 (t0) cc_final: 0.8080 (t0)
REVERT: B   55 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7642 (mppt)
REVERT: B  225 MET cc_start: 0.8349 (mmm) cc_final: 0.7409 (mmm)
REVERT: B  326 LEU cc_start: 0.8391 (mt) cc_final: 0.8056 (mt)
  outliers start: 32
  outliers final: 32
  residues processed: 134
  average time/residue: 0.1846
  time to fit residues: 37.8021
Evaluate side-chains
  147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
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  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  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  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  532 VAL
Chi-restraints excluded: chain B residue  620 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0670
   chunk 78 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0570
   chunk 114 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    1.0240

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.126069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.095872 restraints weight = 17344.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.096255 restraints weight = 14612.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.097089 restraints weight = 12131.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10712  Z= 0.213
  Angle     :  0.601   9.662  14560  Z= 0.298
  Chirality :  0.044   0.161   1726
  Planarity :  0.004   0.051   1816
  Dihedral  :  4.711  40.653   1450
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.77 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.24), residues: 1346
  helix:  1.67 (0.18), residues: 846
  sheet:  1.73 (0.98), residues: 36
  loop : -1.76 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 337 
 PHE   0.012   0.001   PHE A 111 
 TYR   0.010   0.001   TYR B 546 
 ARG   0.006   0.000   ARG A 631 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2659.89 seconds
wall clock time: 48 minutes 57.69 seconds (2937.69 seconds total)