Starting phenix.real_space_refine
on Sun Oct 12 08:04:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7scz_25043/10_2025/7scz_25043.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7scz_25043/10_2025/7scz_25043.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/7scz_25043/10_2025/7scz_25043.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7scz_25043/10_2025/7scz_25043.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7scz_25043/10_2025/7scz_25043.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7scz_25043/10_2025/7scz_25043.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.073
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     294      5.49       5
     S      19      5.16       5
     C    7110      2.51       5
     N    2388      2.21       5
     O    2959      1.98       5
     H   10435      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23205
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "I"
      Number of atoms: 4682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 4682
          Classifications: {'DNA': 147}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 4646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 4646
          Classifications: {'DNA': 147}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 146}
    Chain: "A"
      Number of atoms: 1616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1616
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 1271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1271
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "C"
      Number of atoms: 1733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 1733
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 1461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1461
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 1684
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 1459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 1459
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    Chain: "G"
      Number of atoms: 1667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 1667
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 1450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1450
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "K"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1536
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
  Time building chain proxies: 4.17, per 1000 atoms: 0.18
  Number of scatterers: 23205
  At special positions: 0
  Unit cell: (89.46, 121.41, 120.345, 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      19     16.00
     P     294     15.00
     O    2959      8.00
     N    2388      7.00
     C    7110      6.00
     H   10435      1.00
    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: 2.22
  Conformation dependent library (CDL) restraints added in 382.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1588

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 11 sheets defined
      70.7% alpha, 3.9% beta
      146 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 4.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.793A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.642A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.501A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.644A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.633A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.880A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.142A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 404 through 415
    Processing helix  chain 'K' and resid 433 through 439
    Processing helix  chain 'K' and resid 440 through 449
    Processing helix  chain 'K' and resid 457 through 465
      removed outlier: 3.766A  pdb=" N   ASP K 461 " --> pdb=" O   ASP K 457 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 468 through 473
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.967A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.647A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.649A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.725A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 418 through 420
      removed outlier: 6.351A  pdb=" N   CYS K 429 " --> pdb=" O   VAL K 454 " (cutoff:3.500A)

    444 hydrogen bonds defined for protein.
    1302 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      374 hydrogen bonds
      748 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 6.29

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        0.88 -     1.07: 2390
        1.07 -     1.26: 9404
        1.26 -     1.45: 5394
        1.45 -     1.63: 6804
        1.63 -     1.82: 33
  Bond restraints: 24025
  Sorted by residual:
  bond pdb=" N   LEU K 478 "
       pdb=" H   LEU K 478 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   SER K 479 "
       pdb=" H   SER K 479 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" C6   DC J  69 "
       pdb=" H6   DC J  69 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" NH1 ARG G  88 "
       pdb="HH11 ARG G  88 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" C6   DC I -58 "
       pdb=" H6   DC I -58 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 24020 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.26: 43131
        6.26 -    12.51: 448
       12.51 -    18.77: 1
       18.77 -    25.02: 0
       25.02 -    31.28: 3
  Bond angle restraints: 43583
  Sorted by residual:
  angle pdb=" C   ARG F  17 "
        pdb=" CA  ARG F  17 "
        pdb=" HA  ARG F  17 "
      ideal   model   delta    sigma   weight residual
     109.00   77.72   31.28 3.00e+00 1.11e-01 1.09e+02
  angle pdb=" N   ARG F  17 "
        pdb=" CA  ARG F  17 "
        pdb=" HA  ARG F  17 "
      ideal   model   delta    sigma   weight residual
     110.00   79.30   30.70 3.00e+00 1.11e-01 1.05e+02
  angle pdb=" CB  ARG F  17 "
        pdb=" CA  ARG F  17 "
        pdb=" HA  ARG F  17 "
      ideal   model   delta    sigma   weight residual
     109.00   79.95   29.05 3.00e+00 1.11e-01 9.38e+01
  angle pdb=" N   ARG F  17 "
        pdb=" CA  ARG F  17 "
        pdb=" C   ARG F  17 "
      ideal   model   delta    sigma   weight residual
     109.52  123.02  -13.50 1.55e+00 4.16e-01 7.58e+01
  angle pdb=" C4'  DG I  20 "
        pdb=" C3'  DG I  20 "
        pdb=" O3'  DG I  20 "
      ideal   model   delta    sigma   weight residual
     110.00  120.05  -10.05 1.50e+00 4.44e-01 4.49e+01
  ... (remaining 43578 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.32: 8370
       35.32 -    70.64: 1611
       70.64 -   105.96: 39
      105.96 -   141.28: 1
      141.28 -   176.60: 3
  Dihedral angle restraints: 10024
    sinusoidal: 7285
      harmonic: 2739
  Sorted by residual:
  dihedral pdb=" C   ARG F  17 "
           pdb=" N   ARG F  17 "
           pdb=" CA  ARG F  17 "
           pdb=" CB  ARG F  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.09   19.49     0      2.50e+00 1.60e-01 6.08e+01
  dihedral pdb=" N   ARG F  17 "
           pdb=" C   ARG F  17 "
           pdb=" CA  ARG F  17 "
           pdb=" CB  ARG F  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  141.32  -18.52     0      2.50e+00 1.60e-01 5.49e+01
  dihedral pdb=" CA  SER K 431 "
           pdb=" C   SER K 431 "
           pdb=" N   THR K 432 "
           pdb=" CA  THR K 432 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.38   27.62     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 10021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.163: 2105
       0.163 -    0.326: 114
       0.326 -    0.489: 12
       0.489 -    0.652: 0
       0.652 -    0.815: 1
  Chirality restraints: 2232
  Sorted by residual:
  chirality pdb=" CA  ARG F  17 "
            pdb=" N   ARG F  17 "
            pdb=" C   ARG F  17 "
            pdb=" CB  ARG F  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.70    0.81 2.00e-01 2.50e+01 1.66e+01
  chirality pdb=" C3'  DG I -44 "
            pdb=" C4'  DG I -44 "
            pdb=" O3'  DG I -44 "
            pdb=" C2'  DG I -44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.26   -0.40 2.00e-01 2.50e+01 3.91e+00
  chirality pdb=" CB  THR B  82 "
            pdb=" CA  THR B  82 "
            pdb=" OG1 THR B  82 "
            pdb=" CG2 THR B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.17    0.39 2.00e-01 2.50e+01 3.71e+00
  ... (remaining 2229 not shown)

  Planarity restraints: 2501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT J  38 "   -0.301 2.00e-02 2.50e+03   1.63e-01 7.98e+02
        pdb=" N1   DT J  38 "   -0.094 2.00e-02 2.50e+03
        pdb=" C2   DT J  38 "    0.051 2.00e-02 2.50e+03
        pdb=" O2   DT J  38 "    0.285 2.00e-02 2.50e+03
        pdb=" N3   DT J  38 "   -0.035 2.00e-02 2.50e+03
        pdb=" C4   DT J  38 "   -0.100 2.00e-02 2.50e+03
        pdb=" O4   DT J  38 "   -0.257 2.00e-02 2.50e+03
        pdb=" C5   DT J  38 "    0.035 2.00e-02 2.50e+03
        pdb=" C7   DT J  38 "    0.193 2.00e-02 2.50e+03
        pdb=" C6   DT J  38 "    0.028 2.00e-02 2.50e+03
        pdb=" H3   DT J  38 "    0.087 2.00e-02 2.50e+03
        pdb=" H6   DT J  38 "    0.107 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  47 "   -0.369 2.00e-02 2.50e+03   1.34e-01 6.26e+02
        pdb=" N9   DG J  47 "    0.012 2.00e-02 2.50e+03
        pdb=" C8   DG J  47 "    0.096 2.00e-02 2.50e+03
        pdb=" N7   DG J  47 "    0.103 2.00e-02 2.50e+03
        pdb=" C5   DG J  47 "    0.057 2.00e-02 2.50e+03
        pdb=" C6   DG J  47 "   -0.034 2.00e-02 2.50e+03
        pdb=" O6   DG J  47 "   -0.218 2.00e-02 2.50e+03
        pdb=" N1   DG J  47 "    0.021 2.00e-02 2.50e+03
        pdb=" C2   DG J  47 "    0.077 2.00e-02 2.50e+03
        pdb=" N2   DG J  47 "    0.084 2.00e-02 2.50e+03
        pdb=" N3   DG J  47 "    0.091 2.00e-02 2.50e+03
        pdb=" C4   DG J  47 "    0.080 2.00e-02 2.50e+03
        pdb=" H8   DG J  47 "    0.085 2.00e-02 2.50e+03
        pdb=" H1   DG J  47 "   -0.084 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT J  55 "    0.349 2.00e-02 2.50e+03   1.42e-01 6.07e+02
        pdb=" N1   DT J  55 "   -0.040 2.00e-02 2.50e+03
        pdb=" C2   DT J  55 "   -0.108 2.00e-02 2.50e+03
        pdb=" O2   DT J  55 "   -0.200 2.00e-02 2.50e+03
        pdb=" N3   DT J  55 "   -0.026 2.00e-02 2.50e+03
        pdb=" C4   DT J  55 "    0.045 2.00e-02 2.50e+03
        pdb=" O4   DT J  55 "    0.211 2.00e-02 2.50e+03
        pdb=" C5   DT J  55 "   -0.050 2.00e-02 2.50e+03
        pdb=" C7   DT J  55 "   -0.093 2.00e-02 2.50e+03
        pdb=" C6   DT J  55 "   -0.064 2.00e-02 2.50e+03
        pdb=" H3   DT J  55 "    0.035 2.00e-02 2.50e+03
        pdb=" H6   DT J  55 "   -0.059 2.00e-02 2.50e+03
  ... (remaining 2498 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 1155
        2.18 -     2.79: 36628
        2.79 -     3.39: 62947
        3.39 -     4.00: 89620
        4.00 -     4.60: 128365
  Nonbonded interactions: 318715
  Sorted by model distance:
  nonbonded pdb=" OP1  DA I  28 "
            pdb=" HG1 THR B  80 "
     model   vdw
     1.578 2.450
  nonbonded pdb=" OP1  DG J  28 "
            pdb=" HG1 THR F  80 "
     model   vdw
     1.611 2.450
  nonbonded pdb=" HG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     1.617 2.450
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" HH  TYR F  98 "
     model   vdw
     1.621 2.450
  nonbonded pdb=" HG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     1.628 2.450
  ... (remaining 318710 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 'E' and resid 38 through 133)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 25 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 15 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 33 through 123)
  selection = chain 'H'
}

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:             1.090
  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:             0.130
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     27.590
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
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      :  0.014   0.065  13590  Z= 0.757
  Angle     :  1.915  13.497  19596  Z= 1.269
  Chirality :  0.088   0.815   2232
  Planarity :  0.035   0.172   1456
  Dihedral  : 27.439 176.605   5861
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 0.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.26), residues: 832
  helix:  0.25 (0.19), residues: 580
  sheet: -0.58 (1.52), residues: 6
  loop : -0.05 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  77 
 TYR   0.124   0.021   TYR C  57 
 PHE   0.049   0.012   PHE D  70 
 TRP   0.068   0.027   TRP K 481 
 HIS   0.014   0.004   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.01353 (13590)
  covalent geometry    : angle       1.91481 (19596)
  hydrogen bonds       : bond        0.13010 (  818)
  hydrogen bonds       : angle       6.36587 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.488 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.8343 (t0) cc_final: 0.8023 (t0)
REVERT: B   98 TYR cc_start: 0.8484 (m-10) cc_final: 0.8270 (m-10)
REVERT: C   40 SER cc_start: 0.7653 (p) cc_final: 0.7293 (p)
REVERT: C   90 ASP cc_start: 0.6952 (t70) cc_final: 0.6673 (t70)
REVERT: D   89 ILE cc_start: 0.9265 (mt) cc_final: 0.8903 (mt)
REVERT: E   97 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6935 (mt-10)
REVERT: G   61 GLU cc_start: 0.8342 (tp30) cc_final: 0.8059 (tp30)
REVERT: H   88 THR cc_start: 0.9138 (m) cc_final: 0.8859 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.3785
  time to fit residues: 147.1484
Evaluate side-chains
  196 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
K 476 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.094734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.066845 restraints weight = 67799.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.069929 restraints weight = 23738.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.071867 restraints weight = 13853.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.072916 restraints weight = 10549.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.073510 restraints weight = 9229.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13590  Z= 0.209
  Angle     :  0.708   5.186  19596  Z= 0.433
  Chirality :  0.042   0.405   2232
  Planarity :  0.005   0.046   1456
  Dihedral  : 31.365 170.758   4153
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.43 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.28), residues: 832
  helix:  2.00 (0.21), residues: 585
  sheet: -1.97 (1.32), residues: 11
  loop : -0.14 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 116 
 TYR   0.013   0.001   TYR F  98 
 PHE   0.021   0.002   PHE A  67 
 TRP   0.006   0.002   TRP K 481 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (13590)
  covalent geometry    : angle       0.70835 (19596)
  hydrogen bonds       : bond        0.04989 (  818)
  hydrogen bonds       : angle       3.47825 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 211
  time to evaluate  : 0.501 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: A   73 GLU cc_start: 0.7908 (tp30) cc_final: 0.7645 (tp30)
REVERT: B   74 GLU cc_start: 0.8793 (tt0) cc_final: 0.8182 (mt-10)
REVERT: B   85 ASP cc_start: 0.8872 (m-30) cc_final: 0.8663 (m-30)
REVERT: D   35 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6917 (mt-10)
REVERT: E   50 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8263 (tt0)
REVERT: E   73 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7975 (tm-30)
REVERT: E   94 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7976 (tp30)
REVERT: E  108 ASN cc_start: 0.8723 (t0) cc_final: 0.8246 (t0)
REVERT: G   61 GLU cc_start: 0.8619 (tp30) cc_final: 0.8418 (tp30)
REVERT: G   92 GLU cc_start: 0.8886 (mp0) cc_final: 0.8615 (mp0)
REVERT: H   68 ASP cc_start: 0.8541 (t0) cc_final: 0.8246 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 222
  average time/residue: 0.3057
  time to fit residues: 91.7651
Evaluate side-chains
  200 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 187
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   80 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 106 optimal weight:   20.0000
   chunk 90 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0030
   chunk 21 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.9998

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.092569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.064467 restraints weight = 68559.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.067446 restraints weight = 24472.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.069344 restraints weight = 14516.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.070397 restraints weight = 11136.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.070916 restraints weight = 9745.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13590  Z= 0.222
  Angle     :  0.652   5.053  19596  Z= 0.402
  Chirality :  0.042   0.371   2232
  Planarity :  0.004   0.046   1456
  Dihedral  : 31.041 171.217   4153
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.25 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.28), residues: 832
  helix:  2.31 (0.21), residues: 582
  sheet: -2.09 (1.38), residues: 11
  loop : -0.33 (0.35), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.015   0.002   TYR G  57 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.002   0.001   TRP K 481 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (13590)
  covalent geometry    : angle       0.65152 (19596)
  hydrogen bonds       : bond        0.04270 (  818)
  hydrogen bonds       : angle       3.31205 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.487 
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: symmetry clash
REVERT: A   50 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8130 (mt-10)
REVERT: B   74 GLU cc_start: 0.8934 (tt0) cc_final: 0.8290 (mt-10)
REVERT: D   35 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7257 (mt-10)
REVERT: E  125 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8481 (mm-40)
REVERT: F   25 ASN cc_start: 0.8415 (m110) cc_final: 0.8185 (m110)
REVERT: G   92 GLU cc_start: 0.8963 (mp0) cc_final: 0.8619 (mp0)
REVERT: K  409 LYS cc_start: 0.8273 (tttt) cc_final: 0.8040 (pttp)
  outliers start: 21
  outliers final: 20
  residues processed: 204
  average time/residue: 0.2901
  time to fit residues: 80.7562
Evaluate side-chains
  202 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.091449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.063674 restraints weight = 68842.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.066578 restraints weight = 24432.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.068406 restraints weight = 14475.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.069455 restraints weight = 11118.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.069970 restraints weight = 9726.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.5019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  13590  Z= 0.243
  Angle     :  0.646   8.068  19596  Z= 0.395
  Chirality :  0.043   0.362   2232
  Planarity :  0.004   0.050   1456
  Dihedral  : 30.919 171.981   4153
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.36 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.28), residues: 832
  helix:  2.32 (0.21), residues: 579
  sheet: -1.79 (1.44), residues: 11
  loop : -0.41 (0.35), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 452 
 TYR   0.014   0.002   TYR G  57 
 PHE   0.014   0.001   PHE K 458 
 TRP   0.002   0.001   TRP K 481 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (13590)
  covalent geometry    : angle       0.64617 (19596)
  hydrogen bonds       : bond        0.04142 (  818)
  hydrogen bonds       : angle       3.29331 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 184
  time to evaluate  : 0.490 
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: symmetry clash
REVERT: A   94 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7690 (mm-30)
REVERT: B   74 GLU cc_start: 0.8955 (tt0) cc_final: 0.8493 (mt-10)
REVERT: C   92 GLU cc_start: 0.8424 (mp0) cc_final: 0.7927 (mp0)
REVERT: D   35 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7447 (mt-10)
REVERT: D   42 TYR cc_start: 0.7490 (t80) cc_final: 0.7222 (t80)
REVERT: D  101 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8536 (mm)
REVERT: E   50 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8319 (tt0)
REVERT: G   92 GLU cc_start: 0.8991 (mp0) cc_final: 0.8790 (mp0)
REVERT: G  104 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8939 (mm110)
REVERT: H   93 GLU cc_start: 0.8271 (mp0) cc_final: 0.7412 (mp0)
REVERT: K  409 LYS cc_start: 0.8317 (tttt) cc_final: 0.8065 (pttp)
  outliers start: 26
  outliers final: 22
  residues processed: 200
  average time/residue: 0.2899
  time to fit residues: 79.4005
Evaluate side-chains
  200 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0770
   chunk 20 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.9744

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  76 GLN
** F  75 HIS ** 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 = 0.3519 r_free = 0.3519 target = 0.091689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.064167 restraints weight = 68269.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.067038 restraints weight = 24274.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.068842 restraints weight = 14459.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.069839 restraints weight = 11118.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.070365 restraints weight = 9762.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.5258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13590  Z= 0.213
  Angle     :  0.624   5.219  19596  Z= 0.383
  Chirality :  0.042   0.358   2232
  Planarity :  0.004   0.049   1456
  Dihedral  : 30.739 171.733   4153
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.60 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.28), residues: 832
  helix:  2.45 (0.21), residues: 580
  sheet: -1.63 (1.47), residues: 11
  loop : -0.43 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  92 
 TYR   0.009   0.001   TYR H  40 
 PHE   0.010   0.001   PHE K 458 
 TRP   0.001   0.000   TRP K 481 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (13590)
  covalent geometry    : angle       0.62375 (19596)
  hydrogen bonds       : bond        0.03804 (  818)
  hydrogen bonds       : angle       3.14859 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 190
  time to evaluate  : 0.517 
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   94 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7725 (mm-30)
REVERT: B   74 GLU cc_start: 0.8943 (tt0) cc_final: 0.8469 (mt-10)
REVERT: D   47 GLN cc_start: 0.8621 (mt0) cc_final: 0.8381 (tt0)
REVERT: E   59 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7767 (pm20)
REVERT: G  110 ASN cc_start: 0.8800 (t0) cc_final: 0.8248 (p0)
REVERT: H   93 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7420 (mp0)
REVERT: K  409 LYS cc_start: 0.8322 (tttt) cc_final: 0.8023 (pttm)
  outliers start: 19
  outliers final: 14
  residues processed: 200
  average time/residue: 0.2946
  time to fit residues: 80.7363
Evaluate side-chains
  196 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 107 optimal weight:   20.0000
   chunk 79 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
F  75 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.092444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.064566 restraints weight = 68739.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.067481 restraints weight = 24587.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.069315 restraints weight = 14678.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.070274 restraints weight = 11340.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.070865 restraints weight = 10019.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.5463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13590  Z= 0.197
  Angle     :  0.615   4.942  19596  Z= 0.377
  Chirality :  0.041   0.357   2232
  Planarity :  0.004   0.051   1456
  Dihedral  : 30.624 172.515   4153
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.32 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.28), residues: 832
  helix:  2.58 (0.21), residues: 583
  sheet: -1.28 (1.55), residues: 11
  loop : -0.37 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 129 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.011   0.001   PHE K 458 
 TRP   0.001   0.000   TRP K 481 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (13590)
  covalent geometry    : angle       0.61510 (19596)
  hydrogen bonds       : bond        0.03678 (  818)
  hydrogen bonds       : angle       3.05704 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 0.514 
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   58 THR cc_start: 0.9660 (OUTLIER) cc_final: 0.9454 (t)
REVERT: B   74 GLU cc_start: 0.8902 (tt0) cc_final: 0.8437 (mt-10)
REVERT: D   35 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: D   47 GLN cc_start: 0.8667 (mt0) cc_final: 0.8443 (tt0)
REVERT: E   50 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8312 (tt0)
REVERT: E   59 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7866 (pm20)
REVERT: E  120 MET cc_start: 0.8518 (mtm) cc_final: 0.8280 (mtm)
REVERT: G  110 ASN cc_start: 0.8777 (t0) cc_final: 0.8287 (p0)
REVERT: H   93 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7413 (mp0)
REVERT: K  409 LYS cc_start: 0.8332 (tttt) cc_final: 0.8029 (pttm)
  outliers start: 17
  outliers final: 12
  residues processed: 192
  average time/residue: 0.2909
  time to fit residues: 76.9918
Evaluate side-chains
  196 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 107 optimal weight:   20.0000
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.092698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.064735 restraints weight = 71220.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.067684 restraints weight = 25011.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.069549 restraints weight = 14814.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.070521 restraints weight = 11393.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.071143 restraints weight = 10048.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.5629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13590  Z= 0.213
  Angle     :  0.618   4.978  19596  Z= 0.379
  Chirality :  0.041   0.357   2232
  Planarity :  0.004   0.049   1456
  Dihedral  : 30.552 172.824   4153
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.16 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.28), residues: 832
  helix:  2.51 (0.21), residues: 583
  sheet: -0.71 (1.73), residues: 11
  loop : -0.38 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  92 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.013   0.001   PHE K 458 
 TRP   0.001   0.000   TRP K 481 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (13590)
  covalent geometry    : angle       0.61777 (19596)
  hydrogen bonds       : bond        0.03803 (  818)
  hydrogen bonds       : angle       3.08498 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 188
  time to evaluate  : 0.502 
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: B   74 GLU cc_start: 0.8898 (tt0) cc_final: 0.8555 (mt-10)
REVERT: D   35 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: D   47 GLN cc_start: 0.8631 (mt0) cc_final: 0.8427 (tt0)
REVERT: E   37 LYS cc_start: 0.8521 (pttm) cc_final: 0.8274 (pttt)
REVERT: E   59 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7874 (pm20)
REVERT: G   84 GLN cc_start: 0.8544 (tp40) cc_final: 0.8294 (tp-100)
REVERT: G  110 ASN cc_start: 0.8787 (t0) cc_final: 0.8317 (p0)
REVERT: H   59 MET cc_start: 0.9025 (tpp) cc_final: 0.8722 (tpp)
REVERT: H   93 GLU cc_start: 0.8245 (mp0) cc_final: 0.7471 (mp0)
REVERT: K  409 LYS cc_start: 0.8347 (tttt) cc_final: 0.8021 (pttm)
  outliers start: 19
  outliers final: 13
  residues processed: 198
  average time/residue: 0.2853
  time to fit residues: 77.9846
Evaluate side-chains
  198 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:   20.0000
   chunk 37 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.093271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.065979 restraints weight = 69234.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.068856 restraints weight = 24345.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.070714 restraints weight = 14468.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.071691 restraints weight = 11123.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.072336 restraints weight = 9793.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.5775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13590  Z= 0.177
  Angle     :  0.613   7.716  19596  Z= 0.374
  Chirality :  0.039   0.356   2232
  Planarity :  0.004   0.050   1456
  Dihedral  : 30.455 173.240   4153
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.55 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.29), residues: 832
  helix:  2.69 (0.21), residues: 580
  sheet: -0.82 (1.67), residues: 11
  loop : -0.36 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  92 
 TYR   0.009   0.001   TYR H  40 
 PHE   0.014   0.001   PHE K 458 
 TRP   0.001   0.000   TRP K 481 
 HIS   0.003   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (13590)
  covalent geometry    : angle       0.61277 (19596)
  hydrogen bonds       : bond        0.03489 (  818)
  hydrogen bonds       : angle       2.92765 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 183
  time to evaluate  : 0.499 
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: B   74 GLU cc_start: 0.8891 (tt0) cc_final: 0.8442 (mt-10)
REVERT: D   35 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7410 (mt-10)
REVERT: D   59 MET cc_start: 0.8664 (tpp) cc_final: 0.8452 (tpp)
REVERT: E   37 LYS cc_start: 0.8473 (pttm) cc_final: 0.8229 (pttt)
REVERT: E   59 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7902 (pm20)
REVERT: E  120 MET cc_start: 0.8505 (mtm) cc_final: 0.8297 (mtm)
REVERT: G   84 GLN cc_start: 0.8540 (tp40) cc_final: 0.8293 (tp-100)
REVERT: G  110 ASN cc_start: 0.8757 (t0) cc_final: 0.8353 (p0)
REVERT: H   93 GLU cc_start: 0.8166 (mp0) cc_final: 0.7437 (mp0)
REVERT: K  409 LYS cc_start: 0.8348 (tttt) cc_final: 0.8015 (pttp)
  outliers start: 10
  outliers final: 8
  residues processed: 189
  average time/residue: 0.2905
  time to fit residues: 75.1978
Evaluate side-chains
  186 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 177
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0470
   chunk 47 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 39 optimal weight:    0.1980
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.9882

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
G  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.094343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.067030 restraints weight = 69525.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.069998 restraints weight = 24271.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.071850 restraints weight = 14307.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.072835 restraints weight = 10999.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.073488 restraints weight = 9673.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13590  Z= 0.166
  Angle     :  0.605   7.413  19596  Z= 0.369
  Chirality :  0.039   0.355   2232
  Planarity :  0.003   0.049   1456
  Dihedral  : 30.322 173.455   4153
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.69 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.91 (0.29), residues: 832
  helix:  2.81 (0.21), residues: 583
  sheet: -0.94 (1.60), residues: 11
  loop : -0.22 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.009   0.001   TYR H  42 
 PHE   0.018   0.001   PHE K 458 
 TRP   0.001   0.000   TRP K 481 
 HIS   0.003   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13590)
  covalent geometry    : angle       0.60548 (19596)
  hydrogen bonds       : bond        0.03397 (  818)
  hydrogen bonds       : angle       2.81420 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 183
  time to evaluate  : 0.487 
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: B   74 GLU cc_start: 0.8887 (tt0) cc_final: 0.8471 (mt-10)
REVERT: D   35 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7397 (mt-10)
REVERT: D   59 MET cc_start: 0.8597 (tpp) cc_final: 0.8362 (tpp)
REVERT: E   37 LYS cc_start: 0.8436 (pttm) cc_final: 0.8179 (pttt)
REVERT: E   59 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7844 (pm20)
REVERT: E  120 MET cc_start: 0.8546 (mtm) cc_final: 0.8319 (mtm)
REVERT: G   38 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8200 (m110)
REVERT: G   61 GLU cc_start: 0.8426 (tp30) cc_final: 0.8152 (tp30)
REVERT: G   64 GLU cc_start: 0.7759 (tp30) cc_final: 0.7513 (tp30)
REVERT: G   84 GLN cc_start: 0.8491 (tp40) cc_final: 0.8238 (tp-100)
REVERT: G  110 ASN cc_start: 0.8697 (t0) cc_final: 0.8398 (p0)
REVERT: H   93 GLU cc_start: 0.8126 (mp0) cc_final: 0.7459 (mp0)
REVERT: K  409 LYS cc_start: 0.8356 (tttt) cc_final: 0.8013 (pttp)
  outliers start: 10
  outliers final: 8
  residues processed: 189
  average time/residue: 0.2864
  time to fit residues: 74.2337
Evaluate side-chains
  188 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 178
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.094208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.067092 restraints weight = 69612.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.070009 restraints weight = 24150.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.071873 restraints weight = 14219.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.072897 restraints weight = 10893.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.073455 restraints weight = 9525.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.5974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.210  13590  Z= 0.225
  Angle     :  0.809  59.190  19596  Z= 0.504
  Chirality :  0.040   0.355   2232
  Planarity :  0.003   0.049   1456
  Dihedral  : 30.320 173.460   4153
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.11 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.29), residues: 832
  helix:  2.81 (0.21), residues: 583
  sheet: -0.93 (1.60), residues: 11
  loop : -0.17 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.009   0.001   TYR G  39 
 PHE   0.014   0.001   PHE K 458 
 TRP   0.001   0.000   TRP K 481 
 HIS   0.003   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (13590)
  covalent geometry    : angle       0.80854 (19596)
  hydrogen bonds       : bond        0.03410 (  818)
  hydrogen bonds       : angle       2.82236 ( 2050)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 0.364 
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: B   74 GLU cc_start: 0.8887 (tt0) cc_final: 0.8473 (mt-10)
REVERT: C   92 GLU cc_start: 0.8124 (mp0) cc_final: 0.7769 (mp0)
REVERT: D   35 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7401 (mt-10)
REVERT: D   59 MET cc_start: 0.8599 (tpp) cc_final: 0.8362 (tpp)
REVERT: E   37 LYS cc_start: 0.8449 (pttm) cc_final: 0.8186 (pttt)
REVERT: E   59 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7848 (pm20)
REVERT: E  120 MET cc_start: 0.8550 (mtm) cc_final: 0.8322 (mtm)
REVERT: G   61 GLU cc_start: 0.8433 (tp30) cc_final: 0.8157 (tp30)
REVERT: G   64 GLU cc_start: 0.7764 (tp30) cc_final: 0.7517 (tp30)
REVERT: G   84 GLN cc_start: 0.8495 (tp40) cc_final: 0.8245 (tp-100)
REVERT: G  110 ASN cc_start: 0.8702 (t0) cc_final: 0.8398 (p0)
REVERT: H   93 GLU cc_start: 0.8126 (mp0) cc_final: 0.7461 (mp0)
REVERT: K  409 LYS cc_start: 0.8362 (tttt) cc_final: 0.8019 (pttp)
  outliers start: 11
  outliers final: 10
  residues processed: 185
  average time/residue: 0.2824
  time to fit residues: 71.3466
Evaluate side-chains
  189 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:   30.0000
   chunk 82 optimal weight:   50.0000
   chunk 62 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 102 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.094254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.066980 restraints weight = 69599.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.069891 restraints weight = 24363.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.071773 restraints weight = 14418.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.072849 restraints weight = 11055.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.073384 restraints weight = 9629.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.5990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.288  13590  Z= 0.265
  Angle     :  0.968  59.054  19596  Z= 0.603
  Chirality :  0.044   0.868   2232
  Planarity :  0.003   0.049   1456
  Dihedral  : 30.319 173.464   4153
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 20.25 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.89 (0.29), residues: 832
  helix:  2.77 (0.21), residues: 583
  sheet: -0.93 (1.60), residues: 11
  loop : -0.17 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.008   0.001   TYR G  39 
 PHE   0.013   0.001   PHE A  67 
 TRP   0.001   0.000   TRP K 481 
 HIS   0.003   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (13590)
  covalent geometry    : angle       0.96835 (19596)
  hydrogen bonds       : bond        0.03420 (  818)
  hydrogen bonds       : angle       2.82615 ( 2050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4356.79 seconds
wall clock time: 74 minutes 48.84 seconds (4488.84 seconds total)