Starting phenix.real_space_refine
on Fri Jun  6 15:24:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1m_41817/06_2025/8u1m_41817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1m_41817/06_2025/8u1m_41817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1m_41817/06_2025/8u1m_41817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1m_41817/06_2025/8u1m_41817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1m_41817/06_2025/8u1m_41817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1m_41817/06_2025/8u1m_41817.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    4988      2.51       5
     N    1318      2.21       5
     O    1540      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7882
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3789
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 10, 'TRANS': 452}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 4029
          Classifications: {'peptide': 494}
          Link IDs: {'PTRANS': 11, 'TRANS': 482}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.18, per 1000 atoms: 0.66
  Number of scatterers: 7882
  At special positions: 0
  Unit cell: (90.948, 110.682, 108.108, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      28     16.00
     P       6     15.00
     Mg      2     11.99
     O    1540      8.00
     N    1318      7.00
     C    4988      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: 2.28
  Conformation dependent library (CDL) restraints added in 965.3 milliseconds
  

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1814

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 9 sheets defined
      40.1% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 32
      removed outlier: 3.849A  pdb=" N   MET A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 61
      removed outlier: 4.083A  pdb=" N   ARG A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 68
      removed outlier: 3.790A  pdb=" N   SER A  67 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 102
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.586A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 187 through 193
      removed outlier: 3.570A  pdb=" N   ALA A 190 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   GLU A 191 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 296 through 308
    Processing helix  chain 'A' and resid 370 through 374
    Processing helix  chain 'A' and resid 396 through 419
      removed outlier: 3.853A  pdb=" N   LEU A 400 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 443
      removed outlier: 6.932A  pdb=" N   LYS A 434 " --> pdb=" O   GLU A 430 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ASN A 435 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 436 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 452
      removed outlier: 3.747A  pdb=" N   ALA A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 474
    Processing helix  chain 'A' and resid 516 through 524
    Processing helix  chain 'B' and resid 20 through 32
      removed outlier: 4.353A  pdb=" N   SER B  26 " --> pdb=" O   ALA B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 60
      removed outlier: 4.018A  pdb=" N   ARG B  41 " --> pdb=" O   GLU B  37 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLU B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU B  43 " --> pdb=" O   PHE B  39 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   THR B  60 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
    Processing helix  chain 'B' and resid 94 through 101
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 4.115A  pdb=" N   ALA B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 138
      removed outlier: 3.633A  pdb=" N   TYR B 137 " --> pdb=" O   TYR B 134 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU B 138 " --> pdb=" O   SER B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 193
    Processing helix  chain 'B' and resid 194 through 206
    Processing helix  chain 'B' and resid 296 through 308
    Processing helix  chain 'B' and resid 339 through 343
      removed outlier: 3.912A  pdb=" N   LEU B 342 " --> pdb=" O   PRO B 339 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   PHE B 343 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 339 through 343'
    Processing helix  chain 'B' and resid 364 through 369
      removed outlier: 4.244A  pdb=" N   LEU B 368 " --> pdb=" O   ASN B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 374
    Processing helix  chain 'B' and resid 396 through 421
      removed outlier: 3.887A  pdb=" N   GLU B 420 " --> pdb=" O   GLU B 416 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ASP B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 443
      removed outlier: 6.599A  pdb=" N   LYS B 434 " --> pdb=" O   GLU B 430 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ASN B 435 " --> pdb=" O   GLN B 431 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU B 436 " --> pdb=" O   PHE B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 454
    Processing helix  chain 'B' and resid 468 through 474
    Processing helix  chain 'B' and resid 489 through 495
      removed outlier: 3.920A  pdb=" N   VAL B 493 " --> pdb=" O   ASN B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 504
      removed outlier: 3.873A  pdb=" N   ARG B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   VAL B 502 " --> pdb=" O   PHE B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 521
      removed outlier: 3.690A  pdb=" N   VAL B 521 " --> pdb=" O   ASP B 517 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14
      removed outlier: 4.326A  pdb=" N   ARG B 142 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 278
      removed outlier: 6.674A  pdb=" N   ILE A  73 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   THR A 216 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ILE A  75 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   GLU A 218 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR A  85 " --> pdb=" O   ILE A  76 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR A 179 " --> pdb=" O   ASP A  88 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLY A 178 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 143 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 147 " --> pdb=" O   TYR A 155 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG A 168 " --> pdb=" O   MET A 156 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU B  13 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105
      removed outlier: 3.794A  pdb=" N   ILE A 105 " --> pdb=" O   GLN B  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 322
      removed outlier: 6.351A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 317 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   LEU A 332 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   HIS A 319 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   ALA A 330 " --> pdb=" O   HIS A 319 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   SER A 321 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   PHE A 328 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 380 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER A 382 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 456
    Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 485
    Processing sheet with id=AA7, first strand: chain 'B' and resid 316 through 322
      removed outlier: 4.413A  pdb=" N   ALA B 316 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE B 320 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS B 377 " --> pdb=" O   PHE B 333 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 456
    Processing sheet with id=AA9, first strand: chain 'B' and resid 510 through 512
      removed outlier: 7.449A  pdb=" N   TYR B 483 " --> pdb=" O   VAL B 510 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   MET B 512 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   ILE B 485 " --> pdb=" O   MET B 512 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ILE B 482 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)

    316 hydrogen bonds defined for protein.
    849 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2483
        1.34 -     1.45: 1081
        1.45 -     1.57: 4405
        1.57 -     1.69: 4
        1.69 -     1.81: 48
  Bond restraints: 8021
  Sorted by residual:
  bond pdb=" C5' ATP B 801 "
       pdb=" O5' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.443  1.217  0.226 1.00e-02 1.00e+04 5.12e+02
  bond pdb=" C5' ATP A 801 "
       pdb=" O5' ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.443  1.221  0.222 1.00e-02 1.00e+04 4.92e+02
  bond pdb=" C3' ATP B 801 "
       pdb=" O3' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.423  1.370  0.053 1.10e-02 8.26e+03 2.36e+01
  bond pdb=" C4' ATP B 801 "
       pdb=" O4' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.444  1.397  0.047 1.10e-02 8.26e+03 1.81e+01
  bond pdb=" C1' ATP B 801 "
       pdb=" O4' ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.416  1.361  0.055 1.30e-02 5.92e+03 1.79e+01
  ... (remaining 8016 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.86: 10764
        6.86 -    13.73: 19
       13.73 -    20.59: 4
       20.59 -    27.45: 0
       27.45 -    34.32: 8
  Bond angle restraints: 10795
  Sorted by residual:
  angle pdb=" C5' ATP B 801 "
        pdb=" O5' ATP B 801 "
        pdb=" PA  ATP B 801 "
      ideal   model   delta    sigma   weight residual
     121.27  155.59  -34.32 1.00e+00 1.00e+00 1.18e+03
  angle pdb=" C5' ATP A 801 "
        pdb=" O5' ATP A 801 "
        pdb=" PA  ATP A 801 "
      ideal   model   delta    sigma   weight residual
     121.27  155.25  -33.98 1.00e+00 1.00e+00 1.15e+03
  angle pdb=" C3' ATP B 801 "
        pdb=" C4' ATP B 801 "
        pdb=" C5' ATP B 801 "
      ideal   model   delta    sigma   weight residual
     115.19   83.50   31.69 1.76e+00 3.23e-01 3.24e+02
  angle pdb=" C3' ATP A 801 "
        pdb=" C4' ATP A 801 "
        pdb=" C5' ATP A 801 "
      ideal   model   delta    sigma   weight residual
     115.19   84.32   30.87 1.76e+00 3.23e-01 3.08e+02
  angle pdb=" C4' ATP A 801 "
        pdb=" C5' ATP A 801 "
        pdb=" O5' ATP A 801 "
      ideal   model   delta    sigma   weight residual
     108.83  140.19  -31.36 2.33e+00 1.85e-01 1.82e+02
  ... (remaining 10790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4276
       17.98 -    35.95: 516
       35.95 -    53.93: 112
       53.93 -    71.91: 22
       71.91 -    89.88: 10
  Dihedral angle restraints: 4936
    sinusoidal: 2122
      harmonic: 2814
  Sorted by residual:
  dihedral pdb=" CA  MET B 512 "
           pdb=" C   MET B 512 "
           pdb=" N   THR B 513 "
           pdb=" CA  THR B 513 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.81  -21.19     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  MET A  25 "
           pdb=" C   MET A  25 "
           pdb=" N   SER A  26 "
           pdb=" CA  SER A  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.96   21.04     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  TYR A 456 "
           pdb=" C   TYR A 456 "
           pdb=" N   HIS A 457 "
           pdb=" CA  HIS A 457 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.52   18.48     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 4933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1117
       0.094 -    0.188: 52
       0.188 -    0.282: 4
       0.282 -    0.376: 0
       0.376 -    0.471: 2
  Chirality restraints: 1175
  Sorted by residual:
  chirality pdb=" C4' ATP A 801 "
            pdb=" C3' ATP A 801 "
            pdb=" C5' ATP A 801 "
            pdb=" O4' ATP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.96    0.47 2.00e-01 2.50e+01 5.54e+00
  chirality pdb=" C4' ATP B 801 "
            pdb=" C3' ATP B 801 "
            pdb=" C5' ATP B 801 "
            pdb=" O4' ATP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.96    0.46 2.00e-01 2.50e+01 5.35e+00
  chirality pdb=" C3' ATP A 801 "
            pdb=" C2' ATP A 801 "
            pdb=" C4' ATP A 801 "
            pdb=" O3' ATP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1172 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 311 "   -0.014 2.00e-02 2.50e+03   1.70e-02 7.19e+00
        pdb=" CG  TRP A 311 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 311 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 311 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 311 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 311 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 311 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 311 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 311 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 311 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 211 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A 212 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 212 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 212 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 177 "   -0.136 9.50e-02 1.11e+02   6.11e-02 2.39e+00
        pdb=" NE  ARG A 177 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 177 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 177 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 177 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 69
        2.40 -     3.03: 4825
        3.03 -     3.65: 13142
        3.65 -     4.28: 19190
        4.28 -     4.90: 29932
  Nonbonded interactions: 67158
  Sorted by model distance:
  nonbonded pdb=" CB  SER B 159 "
            pdb=" CD1 PHE B 165 "
     model   vdw
     1.781 3.740
  nonbonded pdb=" O2G ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.938 2.170
  nonbonded pdb=" O3A ATP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.967 2.170
  nonbonded pdb=" O2B ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.971 2.170
  nonbonded pdb=" O2A ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.028 2.170
  ... (remaining 67153 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 10 through 490 or resid 507 through 530 or resid 801 throu \ 
gh 802))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.870
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
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      :  0.005   0.226   8021  Z= 0.425
  Angle     :  1.167  34.316  10795  Z= 0.717
  Chirality :  0.048   0.471   1175
  Planarity :  0.004   0.061   1374
  Dihedral  : 16.519  89.885   3122
  Min Nonbonded Distance : 1.781

Molprobity Statistics.
  All-atom Clashscore : 23.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 18.79 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.27), residues: 947
  helix:  0.01 (0.30), residues: 313
  sheet: -1.23 (0.42), residues: 156
  loop : -1.10 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP A 311 
 HIS   0.007   0.001   HIS A 314 
 PHE   0.010   0.001   PHE A 208 
 TYR   0.015   0.002   TYR A 372 
 ARG   0.006   0.000   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22434 (  316)
  hydrogen bonds       : angle       9.26347 (  849)
  covalent geometry    : bond        0.00519 ( 8021)
  covalent geometry    : angle       1.16714 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 MET cc_start: 0.5009 (mmt) cc_final: 0.4370 (mmt)
REVERT: B  362 MET cc_start: 0.4810 (tpt) cc_final: 0.4181 (tpp)
REVERT: B  475 MET cc_start: 0.4829 (mtm) cc_final: 0.4611 (ptp)
  outliers start: 3
  outliers final: 0
  residues processed: 36
  average time/residue: 0.2209
  time to fit residues: 11.5907
Evaluate side-chains
  31 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 72 optimal weight:   30.0000
   chunk 39 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 86 optimal weight:    9.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 435 ASN
A 446 ASN
B 150 ASN
** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 GLN
** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 ASN
B 406 ASN
B 431 GLN
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.041613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.033879 restraints weight = 95703.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.034594 restraints weight = 69613.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.035109 restraints weight = 55482.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8021  Z= 0.230
  Angle     :  0.691   7.831  10795  Z= 0.371
  Chirality :  0.044   0.163   1175
  Planarity :  0.004   0.046   1374
  Dihedral  : 10.541  88.615   1110
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 23.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.56 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.27), residues: 947
  helix: -0.00 (0.29), residues: 320
  sheet: -1.52 (0.40), residues: 162
  loop : -1.36 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 311 
 HIS   0.009   0.002   HIS A 314 
 PHE   0.012   0.002   PHE A  84 
 TYR   0.017   0.002   TYR B 519 
 ARG   0.006   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05151 (  316)
  hydrogen bonds       : angle       7.42195 (  849)
  covalent geometry    : bond        0.00481 ( 8021)
  covalent geometry    : angle       0.69096 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 31
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8751 (ppp) cc_final: 0.8444 (ppp)
REVERT: B   84 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7152 (t80)
  outliers start: 23
  outliers final: 11
  residues processed: 52
  average time/residue: 0.1691
  time to fit residues: 13.4595
Evaluate side-chains
  43 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  275 TYR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  507 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 6 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 82 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 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 = 0.3855 r_free = 0.3855 target = 0.040078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.032464 restraints weight = 100866.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.033187 restraints weight = 72711.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.033708 restraints weight = 57558.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8021  Z= 0.272
  Angle     :  0.756   9.168  10795  Z= 0.401
  Chirality :  0.046   0.171   1175
  Planarity :  0.005   0.064   1374
  Dihedral  : 10.555  87.314   1110
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 28.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 17.87 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.26), residues: 947
  helix: -0.29 (0.29), residues: 316
  sheet: -1.95 (0.39), residues: 164
  loop : -1.49 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 311 
 HIS   0.009   0.002   HIS B 205 
 PHE   0.012   0.002   PHE A  84 
 TYR   0.019   0.003   TYR B 519 
 ARG   0.007   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04758 (  316)
  hydrogen bonds       : angle       7.22640 (  849)
  covalent geometry    : bond        0.00574 ( 8021)
  covalent geometry    : angle       0.75552 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 31
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8277 (t0)
REVERT: A  156 MET cc_start: 0.8751 (ppp) cc_final: 0.8273 (ppp)
REVERT: B   24 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9161 (mt)
REVERT: B   84 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7275 (t80)
REVERT: B  165 PHE cc_start: 0.7313 (m-80) cc_final: 0.7049 (m-80)
REVERT: B  300 TYR cc_start: 0.2505 (OUTLIER) cc_final: 0.2123 (m-10)
REVERT: B  421 ASP cc_start: 0.9345 (OUTLIER) cc_final: 0.9105 (p0)
REVERT: B  512 MET cc_start: 0.6050 (ppp) cc_final: 0.5792 (ppp)
  outliers start: 44
  outliers final: 19
  residues processed: 73
  average time/residue: 0.1700
  time to fit residues: 18.5752
Evaluate side-chains
  55 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 31
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  275 TYR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  507 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 82 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 HIS ** 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 = 0.3908 r_free = 0.3908 target = 0.041511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.033766 restraints weight = 96364.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.034531 restraints weight = 69206.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.035054 restraints weight = 54729.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8021  Z= 0.154
  Angle     :  0.642  12.806  10795  Z= 0.337
  Chirality :  0.043   0.186   1175
  Planarity :  0.004   0.052   1374
  Dihedral  :  9.934  84.737   1110
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 22.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.07 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.27), residues: 947
  helix:  0.00 (0.30), residues: 320
  sheet: -1.90 (0.39), residues: 169
  loop : -1.38 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 311 
 HIS   0.007   0.001   HIS A 314 
 PHE   0.016   0.001   PHE B 333 
 TYR   0.018   0.002   TYR A 372 
 ARG   0.005   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  316)
  hydrogen bonds       : angle       6.76723 (  849)
  covalent geometry    : bond        0.00331 ( 8021)
  covalent geometry    : angle       0.64241 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 34
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8954 (tppt)
REVERT: A  156 MET cc_start: 0.8759 (ppp) cc_final: 0.8261 (ppp)
REVERT: B  125 MET cc_start: 0.6437 (pmm) cc_final: 0.6001 (pmm)
REVERT: B  165 PHE cc_start: 0.7103 (m-80) cc_final: 0.6865 (m-80)
REVERT: B  300 TYR cc_start: 0.1780 (OUTLIER) cc_final: 0.1568 (m-10)
REVERT: B  421 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.9061 (p0)
  outliers start: 29
  outliers final: 19
  residues processed: 61
  average time/residue: 0.2019
  time to fit residues: 17.7113
Evaluate side-chains
  53 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 31
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  275 TYR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  507 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 69 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 63 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0030
   overall best weight:    2.5796

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 282 ASN
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.041724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.034027 restraints weight = 97017.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.034804 restraints weight = 69658.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.035327 restraints weight = 54866.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8021  Z= 0.142
  Angle     :  0.621  13.593  10795  Z= 0.324
  Chirality :  0.042   0.153   1175
  Planarity :  0.003   0.050   1374
  Dihedral  :  9.843  86.330   1110
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 20.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.95 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.27), residues: 947
  helix:  0.16 (0.30), residues: 320
  sheet: -1.84 (0.39), residues: 168
  loop : -1.37 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 311 
 HIS   0.007   0.001   HIS A 314 
 PHE   0.014   0.001   PHE B 333 
 TYR   0.018   0.002   TYR A 372 
 ARG   0.005   0.000   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  316)
  hydrogen bonds       : angle       6.56763 (  849)
  covalent geometry    : bond        0.00306 ( 8021)
  covalent geometry    : angle       0.62141 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 32
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8291 (t0)
REVERT: A   93 MET cc_start: 0.1445 (mmt) cc_final: 0.0974 (mmt)
REVERT: A  125 MET cc_start: 0.8320 (mmm) cc_final: 0.8111 (mmm)
REVERT: A  156 MET cc_start: 0.8689 (ppp) cc_final: 0.8299 (ppp)
REVERT: B   24 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9073 (mt)
REVERT: B  125 MET cc_start: 0.6543 (pmm) cc_final: 0.6122 (pmm)
REVERT: B  156 MET cc_start: 0.4698 (tpp) cc_final: 0.4484 (mmm)
REVERT: B  165 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6888 (m-80)
REVERT: B  300 TYR cc_start: 0.1548 (OUTLIER) cc_final: 0.1339 (m-10)
REVERT: B  362 MET cc_start: 0.5439 (tpt) cc_final: 0.4884 (mmt)
REVERT: B  421 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.9050 (p0)
REVERT: B  512 MET cc_start: 0.5751 (ppp) cc_final: 0.5485 (ppp)
REVERT: B  525 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8865 (ppt170)
  outliers start: 39
  outliers final: 24
  residues processed: 68
  average time/residue: 0.2239
  time to fit residues: 21.5619
Evaluate side-chains
  62 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 32
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  165 PHE
Chi-restraints excluded: chain B residue  275 TYR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  525 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 57 optimal weight:   30.0000
   chunk 62 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 GLN
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.040649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.032969 restraints weight = 98653.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.033709 restraints weight = 71260.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.034229 restraints weight = 56364.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8021  Z= 0.203
  Angle     :  0.678  13.968  10795  Z= 0.353
  Chirality :  0.043   0.142   1175
  Planarity :  0.004   0.060   1374
  Dihedral  : 10.137  87.619   1110
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 24.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 19.95 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.27), residues: 947
  helix:  0.10 (0.30), residues: 317
  sheet: -1.94 (0.39), residues: 166
  loop : -1.42 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 311 
 HIS   0.008   0.002   HIS A 314 
 PHE   0.013   0.001   PHE B 333 
 TYR   0.015   0.002   TYR B 471 
 ARG   0.007   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  316)
  hydrogen bonds       : angle       6.64029 (  849)
  covalent geometry    : bond        0.00434 ( 8021)
  covalent geometry    : angle       0.67835 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 32
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8295 (t0)
REVERT: A  156 MET cc_start: 0.8752 (ppp) cc_final: 0.8407 (ppp)
REVERT: B   24 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9177 (mt)
REVERT: B  125 MET cc_start: 0.6670 (pmm) cc_final: 0.6284 (pmm)
REVERT: B  128 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6865 (tm-30)
REVERT: B  156 MET cc_start: 0.4808 (tpp) cc_final: 0.4537 (mmm)
REVERT: B  165 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6944 (m-80)
REVERT: B  300 TYR cc_start: 0.1894 (OUTLIER) cc_final: 0.1673 (m-10)
REVERT: B  362 MET cc_start: 0.5429 (tpt) cc_final: 0.4323 (tpp)
REVERT: B  421 ASP cc_start: 0.9301 (OUTLIER) cc_final: 0.9030 (p0)
  outliers start: 47
  outliers final: 28
  residues processed: 75
  average time/residue: 0.2084
  time to fit residues: 22.2475
Evaluate side-chains
  65 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 31
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  221 ARG
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  165 PHE
Chi-restraints excluded: chain B residue  275 TYR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  300 TYR
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  518 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    0.0870
   chunk 35 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    4.0166

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 GLN
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.040883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.033255 restraints weight = 98377.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.033997 restraints weight = 71264.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.034525 restraints weight = 56370.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8021  Z= 0.180
  Angle     :  0.659  14.603  10795  Z= 0.343
  Chirality :  0.042   0.142   1175
  Planarity :  0.004   0.055   1374
  Dihedral  : 10.078  87.509   1110
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 22.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.81 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.27), residues: 947
  helix:  0.11 (0.30), residues: 317
  sheet: -1.97 (0.39), residues: 161
  loop : -1.38 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 311 
 HIS   0.006   0.001   HIS A 314 
 PHE   0.015   0.001   PHE B  17 
 TYR   0.024   0.002   TYR A 275 
 ARG   0.006   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  316)
  hydrogen bonds       : angle       6.56798 (  849)
  covalent geometry    : bond        0.00388 ( 8021)
  covalent geometry    : angle       0.65942 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 31
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.2076 (mmt) cc_final: 0.1429 (mmt)
REVERT: A  156 MET cc_start: 0.8724 (ppp) cc_final: 0.8416 (ppp)
REVERT: A  334 VAL cc_start: 0.3239 (OUTLIER) cc_final: 0.2937 (p)
REVERT: B  125 MET cc_start: 0.6752 (pmm) cc_final: 0.6392 (pmm)
REVERT: B  156 MET cc_start: 0.4783 (tpp) cc_final: 0.4502 (mmm)
REVERT: B  362 MET cc_start: 0.5429 (tpt) cc_final: 0.4352 (tpp)
REVERT: B  421 ASP cc_start: 0.9280 (OUTLIER) cc_final: 0.9007 (p0)
REVERT: B  512 MET cc_start: 0.5856 (ppp) cc_final: 0.5609 (ppp)
  outliers start: 39
  outliers final: 26
  residues processed: 67
  average time/residue: 0.1904
  time to fit residues: 18.5047
Evaluate side-chains
  59 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 31
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  275 TYR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  518 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0170
   chunk 86 optimal weight:    8.9990
   chunk 81 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0020
   overall best weight:    1.8032

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 HIS
B 441 HIS
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.042069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.034336 restraints weight = 96313.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.035112 restraints weight = 69092.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.035645 restraints weight = 54404.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8021  Z= 0.129
  Angle     :  0.610  12.013  10795  Z= 0.321
  Chirality :  0.042   0.144   1175
  Planarity :  0.003   0.041   1374
  Dihedral  :  9.786  88.659   1110
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.51 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.27), residues: 947
  helix:  0.28 (0.30), residues: 321
  sheet: -1.92 (0.39), residues: 166
  loop : -1.36 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 311 
 HIS   0.005   0.001   HIS A 314 
 PHE   0.016   0.001   PHE B 333 
 TYR   0.019   0.002   TYR B 300 
 ARG   0.004   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  316)
  hydrogen bonds       : angle       6.35369 (  849)
  covalent geometry    : bond        0.00285 ( 8021)
  covalent geometry    : angle       0.60995 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 33
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.2084 (mmt) cc_final: 0.1273 (mmt)
REVERT: A  156 MET cc_start: 0.8705 (ppp) cc_final: 0.8418 (ppp)
REVERT: B  125 MET cc_start: 0.6751 (pmm) cc_final: 0.6384 (pmm)
REVERT: B  156 MET cc_start: 0.4735 (tpp) cc_final: 0.4463 (mmm)
REVERT: B  362 MET cc_start: 0.5333 (tpt) cc_final: 0.4531 (tpp)
REVERT: B  421 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.9001 (p0)
REVERT: B  512 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.5166 (ppp)
  outliers start: 32
  outliers final: 25
  residues processed: 62
  average time/residue: 0.2013
  time to fit residues: 18.1275
Evaluate side-chains
  59 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 32
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  150 ASN
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  275 TYR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  512 MET
Chi-restraints excluded: chain B residue  525 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0070
   chunk 68 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 87 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    0.9602

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 GLN
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.043009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.035100 restraints weight = 96945.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.035913 restraints weight = 69277.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.036468 restraints weight = 54322.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8021  Z= 0.112
  Angle     :  0.599  10.572  10795  Z= 0.312
  Chirality :  0.042   0.146   1175
  Planarity :  0.003   0.037   1374
  Dihedral  :  9.618  87.794   1110
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 23.55 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.27), residues: 947
  helix:  0.37 (0.30), residues: 321
  sheet: -1.84 (0.40), residues: 165
  loop : -1.21 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 311 
 HIS   0.005   0.001   HIS B 314 
 PHE   0.021   0.001   PHE B 333 
 TYR   0.023   0.001   TYR A 275 
 ARG   0.003   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  316)
  hydrogen bonds       : angle       6.14621 (  849)
  covalent geometry    : bond        0.00244 ( 8021)
  covalent geometry    : angle       0.59875 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 32
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8647 (ppp) cc_final: 0.8370 (ppp)
REVERT: B  125 MET cc_start: 0.6828 (pmm) cc_final: 0.6397 (pmm)
REVERT: B  156 MET cc_start: 0.4773 (tpp) cc_final: 0.4526 (mmm)
REVERT: B  421 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8872 (p0)
REVERT: B  475 MET cc_start: 0.4162 (mtt) cc_final: 0.3876 (ptp)
REVERT: B  512 MET cc_start: 0.5393 (OUTLIER) cc_final: 0.4411 (ppp)
  outliers start: 24
  outliers final: 18
  residues processed: 53
  average time/residue: 0.2065
  time to fit residues: 16.0227
Evaluate side-chains
  50 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 30
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  512 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 77 optimal weight:   20.0000
   chunk 92 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 20 optimal weight:    0.1980
   chunk 93 optimal weight:    0.6980
   chunk 33 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 GLN
B 128 GLN
** B 492 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 = 0.3920 r_free = 0.3920 target = 0.041982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.034233 restraints weight = 97788.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.035020 restraints weight = 70252.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.035557 restraints weight = 55184.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8021  Z= 0.150
  Angle     :  0.643  11.006  10795  Z= 0.331
  Chirality :  0.042   0.139   1175
  Planarity :  0.003   0.043   1374
  Dihedral  :  9.790  88.009   1110
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 23.90 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.27), residues: 947
  helix:  0.39 (0.30), residues: 321
  sheet: -1.89 (0.39), residues: 166
  loop : -1.22 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A 311 
 HIS   0.005   0.001   HIS A 314 
 PHE   0.018   0.001   PHE B 333 
 TYR   0.028   0.002   TYR A 275 
 ARG   0.004   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03534 (  316)
  hydrogen bonds       : angle       6.14442 (  849)
  covalent geometry    : bond        0.00328 ( 8021)
  covalent geometry    : angle       0.64324 (10795)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 32
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.0328 (mtp) cc_final: -0.0588 (mtm)
REVERT: A  156 MET cc_start: 0.8606 (ppp) cc_final: 0.8356 (ppp)
REVERT: A  475 MET cc_start: 0.8398 (tmm) cc_final: 0.8061 (ttt)
REVERT: B  125 MET cc_start: 0.6918 (pmm) cc_final: 0.6516 (pmm)
REVERT: B  156 MET cc_start: 0.4620 (tpp) cc_final: 0.4349 (mmm)
REVERT: B  421 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8960 (p0)
REVERT: B  512 MET cc_start: 0.5471 (ppp) cc_final: 0.5168 (ppp)
  outliers start: 26
  outliers final: 23
  residues processed: 58
  average time/residue: 0.1844
  time to fit residues: 15.8757
Evaluate side-chains
  54 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 30
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  309 ASN
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  518 GLU
Chi-restraints excluded: chain B residue  525 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 86 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 89 optimal weight:   40.0000
   chunk 51 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 11 optimal weight:    7.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 154 GLN
** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 ASN
** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 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 = 0.3840 r_free = 0.3840 target = 0.039854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.032304 restraints weight = 101458.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.033019 restraints weight = 73380.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.033522 restraints weight = 58271.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   8021  Z= 0.309
  Angle     :  0.849  12.193  10795  Z= 0.439
  Chirality :  0.048   0.256   1175
  Planarity :  0.005   0.068   1374
  Dihedral  : 10.798  89.310   1110
  Min Nonbonded Distance : 1.740

Molprobity Statistics.
  All-atom Clashscore : 31.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.43 %
    Favored  : 72.85 %
  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: -1.66 (0.27), residues: 947
  helix: -0.15 (0.28), residues: 317
  sheet: -2.18 (0.40), residues: 154
  loop : -1.31 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.004   TRP A 311 
 HIS   0.008   0.002   HIS A 314 
 PHE   0.017   0.002   PHE B 333 
 TYR   0.033   0.003   TYR A 275 
 ARG   0.008   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  316)
  hydrogen bonds       : angle       6.71225 (  849)
  covalent geometry    : bond        0.00657 ( 8021)
  covalent geometry    : angle       0.84922 (10795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3385.65 seconds
wall clock time: 59 minutes 41.95 seconds (3581.95 seconds total)