Starting phenix.real_space_refine
on Wed Jul 30 18:19:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g6h_29769/07_2025/8g6h_29769.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g6h_29769/07_2025/8g6h_29769.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g6h_29769/07_2025/8g6h_29769.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g6h_29769/07_2025/8g6h_29769.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g6h_29769/07_2025/8g6h_29769.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g6h_29769/07_2025/8g6h_29769.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.017
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: 5
    Type Number    sf(0)   Gaussians
     P     314      5.49       5
     S      13      5.16       5
     C    7171      2.51       5
     N    2423      2.21       5
     O    3053      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12974
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 803
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MLY:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 742
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MLY:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 723
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 3196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3196
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "J"
      Number of atoms: 3241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3241
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "K"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 582
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LEU K  73 " occ=0.52
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.52
  Time building chain proxies: 8.13, per 1000 atoms: 0.63
  Number of scatterers: 12974
  At special positions: 0
  Unit cell: (124.696, 95.048, 133.416, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     P     314     15.00
     O    3053      8.00
     N    2423      7.00
     C    7171      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.88
  Conformation dependent library (CDL) restraints added in 953.7 milliseconds
  

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 11 sheets defined
      69.2% alpha, 5.1% beta
      157 base pairs and 282 stacking pairs defined.
    Time for finding SS restraints: 5.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.657A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.539A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.145A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.554A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.622A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.575A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 3.789A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.623A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.510A  pdb=" N   ALA E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.083A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.590A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.584A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.569A  pdb=" N   MET H  56 " --> pdb=" O   SER H  52 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.955A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 35
    Processing helix  chain 'K' and resid 55 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.716A  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 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.092A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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
      removed outlier: 6.804A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.774A  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: 6.968A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (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 12 through 16
      removed outlier: 8.988A  pdb=" N   LEU K  67 " --> pdb=" O   GLN K   2 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   PHE K   4 " --> pdb=" O   LEU K  67 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   LEU K  69 " --> pdb=" O   PHE K   4 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS K   6 " --> pdb=" O   LEU K  69 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   LEU K  71 " --> pdb=" O   LYS K   6 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      405 hydrogen bonds
      810 hydrogen bond angles
      0 basepair planarities
      157 basepair parallelities
      282 stacking parallelities
  Total time for adding SS restraints: 5.14

  Time building geometry restraints manager: 3.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2532
        1.33 -     1.45: 4475
        1.45 -     1.57: 6185
        1.57 -     1.69: 626
        1.69 -     1.81: 24
  Bond restraints: 13842
  Sorted by residual:
  bond pdb=" P    DA J  16 "
       pdb=" OP2  DA J  16 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.45e+00
  bond pdb=" P    DG J  27 "
       pdb=" OP2  DG J  27 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" P    DG J  27 "
       pdb=" OP1  DG J  27 "
    ideal  model  delta    sigma   weight residual
    1.480  1.513 -0.033 2.00e-02 2.50e+03 2.70e+00
  bond pdb=" P    DA J  16 "
       pdb=" OP1  DA J  16 "
    ideal  model  delta    sigma   weight residual
    1.480  1.512 -0.032 2.00e-02 2.50e+03 2.53e+00
  bond pdb=" CB  GLN K  31 "
       pdb=" CG  GLN K  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.55e+00
  ... (remaining 13837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 19651
        1.75 -     3.49: 372
        3.49 -     5.24: 17
        5.24 -     6.98: 8
        6.98 -     8.73: 2
  Bond angle restraints: 20050
  Sorted by residual:
  angle pdb=" C3'  DA J  26 "
        pdb=" O3'  DA J  26 "
        pdb=" P    DG J  27 "
      ideal   model   delta    sigma   weight residual
     120.20  113.74    6.46 1.50e+00 4.44e-01 1.86e+01
  angle pdb=" O3'  DG J  27 "
        pdb=" P    DA J  28 "
        pdb=" O5'  DA J  28 "
      ideal   model   delta    sigma   weight residual
     104.00   98.25    5.75 1.50e+00 4.44e-01 1.47e+01
  angle pdb=" O3'  DA J  16 "
        pdb=" P    DA J  17 "
        pdb=" O5'  DA J  17 "
      ideal   model   delta    sigma   weight residual
     104.00   98.58    5.42 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" C3'  DT J  15 "
        pdb=" O3'  DT J  15 "
        pdb=" P    DA J  16 "
      ideal   model   delta    sigma   weight residual
     120.20  114.95    5.25 1.50e+00 4.44e-01 1.22e+01
  angle pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
        pdb=" CB  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     113.65  109.16    4.49 1.47e+00 4.63e-01 9.35e+00
  ... (remaining 20045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 5957
       35.81 -    71.61: 1534
       71.61 -   107.42: 11
      107.42 -   143.23: 3
      143.23 -   179.03: 1
  Dihedral angle restraints: 7506
    sinusoidal: 5116
      harmonic: 2390
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.97  179.03     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I   4 "
           pdb=" C3'  DC I   4 "
           pdb=" O3'  DC I   4 "
           pdb=" P    DC I   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   88.60  131.40     1      3.50e+01 8.16e-04 1.30e+01
  dihedral pdb=" C4'  DC J  34 "
           pdb=" C3'  DC J  34 "
           pdb=" O3'  DC J  34 "
           pdb=" P    DT J  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   89.63  130.37     1      3.50e+01 8.16e-04 1.29e+01
  ... (remaining 7503 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 2237
       0.088 -    0.176: 52
       0.176 -    0.264: 0
       0.264 -    0.352: 0
       0.352 -    0.440: 2
  Chirality restraints: 2291
  Sorted by residual:
  chirality pdb=" P    DG J  27 "
            pdb=" OP1  DG J  27 "
            pdb=" OP2  DG J  27 "
            pdb=" O5'  DG J  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.79   -0.44 2.00e-01 2.50e+01 4.84e+00
  chirality pdb=" P    DA J  16 "
            pdb=" OP1  DA J  16 "
            pdb=" OP2  DA J  16 "
            pdb=" O5'  DA J  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.77   -0.43 2.00e-01 2.50e+01 4.58e+00
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 2288 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  24 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   ASP B  24 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ASP B  24 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B  25 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.025 2.00e-02 2.50e+03   1.05e-02 3.33e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  26 "   -0.024 2.00e-02 2.50e+03   9.95e-03 2.97e+00
        pdb=" N9   DG I  26 "    0.022 2.00e-02 2.50e+03
        pdb=" C8   DG I  26 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DG I  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  26 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  26 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  26 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  26 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2198
        2.78 -     3.31: 10604
        3.31 -     3.84: 24244
        3.84 -     4.37: 29377
        4.37 -     4.90: 42149
  Nonbonded interactions: 108572
  Sorted by model distance:
  nonbonded pdb=" N   GLU C  91 "
            pdb=" OE1 GLU C  91 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OG1 THR B  73 "
            pdb=" OD2 ASP B  85 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   GLN K  62 "
            pdb=" OG  SER K  65 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   GLU K  16 "
            pdb=" NZ  LYS K  29 "
     model   vdw
     2.291 3.120
  ... (remaining 108567 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' and resid 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 29 through 121)
  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=0.52 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     35.470
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
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      :  0.003   0.037  13842  Z= 0.160
  Angle     :  0.562   8.726  20050  Z= 0.343
  Chirality :  0.036   0.440   2291
  Planarity :  0.004   0.037   1450
  Dihedral  : 28.192 179.033   5962
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.90 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.30), residues: 800
  helix:  2.65 (0.22), residues: 535
  sheet:  1.95 (0.98), residues: 25
  loop : -0.30 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS K  68 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.012   0.001   TYR F  51 
 ARG   0.002   0.000   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11614 (  828)
  hydrogen bonds       : angle       3.67302 ( 2046)
  covalent geometry    : bond        0.00327 (13842)
  covalent geometry    : angle       0.56232 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.040 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.3539
  time to fit residues: 58.1136
Evaluate side-chains
  123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
D  92 GLN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.116857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.083193 restraints weight = 21446.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.21
r_work: 0.2835 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.0666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047  13842  Z= 0.314
  Angle     :  0.590   6.082  20050  Z= 0.356
  Chirality :  0.038   0.142   2291
  Planarity :  0.005   0.044   1450
  Dihedral  : 30.268 175.843   4342
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.88 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.30), residues: 800
  helix:  2.63 (0.22), residues: 542
  sheet:  1.66 (1.01), residues: 26
  loop : -0.50 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS K  68 
 PHE   0.011   0.002   PHE H  67 
 TYR   0.010   0.002   TYR E  54 
 ARG   0.003   0.000   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07786 (  828)
  hydrogen bonds       : angle       3.10641 ( 2046)
  covalent geometry    : bond        0.00715 (13842)
  covalent geometry    : angle       0.59015 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 1.083 
Fit side-chains
REVERT: B   93 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7375 (mp10)
REVERT: C   64 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8263 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 133
  average time/residue: 0.3447
  time to fit residues: 60.5757
Evaluate side-chains
  136 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   66 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 86 optimal weight:   20.0000
   chunk 34 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.117786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.084032 restraints weight = 21639.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.16
r_work: 0.2852 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.0624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  13842  Z= 0.209
  Angle     :  0.561   6.617  20050  Z= 0.342
  Chirality :  0.035   0.129   2291
  Planarity :  0.004   0.040   1450
  Dihedral  : 30.307 176.340   4342
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.02 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.30), residues: 800
  helix:  2.69 (0.22), residues: 542
  sheet:  2.02 (1.01), residues: 25
  loop : -0.50 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS K  68 
 PHE   0.010   0.001   PHE F  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.003   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06717 (  828)
  hydrogen bonds       : angle       3.08090 ( 2046)
  covalent geometry    : bond        0.00453 (13842)
  covalent geometry    : angle       0.56143 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.920 
Fit side-chains
REVERT: B   93 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7360 (mp10)
REVERT: E  131 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8903 (mtp85)
REVERT: H   98 LEU cc_start: 0.9359 (mm) cc_final: 0.9112 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 133
  average time/residue: 0.3470
  time to fit residues: 60.6228
Evaluate side-chains
  138 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   66 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.116448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.082679 restraints weight = 21317.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.19
r_work: 0.2826 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.0908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  13842  Z= 0.328
  Angle     :  0.599   5.812  20050  Z= 0.361
  Chirality :  0.039   0.144   2291
  Planarity :  0.005   0.042   1450
  Dihedral  : 30.388 174.879   4342
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.59 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.30), residues: 800
  helix:  2.55 (0.22), residues: 542
  sheet:  2.08 (1.15), residues: 23
  loop : -0.61 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E  39 
 PHE   0.011   0.002   PHE H  67 
 TYR   0.011   0.002   TYR E  54 
 ARG   0.003   0.000   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07835 (  828)
  hydrogen bonds       : angle       3.06432 ( 2046)
  covalent geometry    : bond        0.00748 (13842)
  covalent geometry    : angle       0.59944 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8041 (mtp180)
REVERT: B   93 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7414 (mp10)
REVERT: C   64 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8189 (tt0)
REVERT: C   73 ASN cc_start: 0.8393 (m-40) cc_final: 0.8151 (t0)
REVERT: E  131 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8947 (mtp85)
REVERT: G   36 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8605 (mtpp)
REVERT: H   98 LEU cc_start: 0.9392 (mm) cc_final: 0.9139 (mm)
REVERT: K    1 MET cc_start: 0.6271 (tmm) cc_final: 0.5911 (tmm)
  outliers start: 17
  outliers final: 9
  residues processed: 140
  average time/residue: 0.3675
  time to fit residues: 66.9091
Evaluate side-chains
  147 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    4 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.118134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.084493 restraints weight = 21503.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.16
r_work: 0.2867 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.0802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13842  Z= 0.175
  Angle     :  0.566   5.936  20050  Z= 0.344
  Chirality :  0.034   0.147   2291
  Planarity :  0.004   0.038   1450
  Dihedral  : 30.435 176.000   4342
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.02 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.30), residues: 800
  helix:  2.70 (0.22), residues: 542
  sheet:  2.08 (1.15), residues: 23
  loop : -0.47 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS K  68 
 PHE   0.010   0.001   PHE F  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.004   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06244 (  828)
  hydrogen bonds       : angle       3.04935 ( 2046)
  covalent geometry    : bond        0.00363 (13842)
  covalent geometry    : angle       0.56630 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.939 
Fit side-chains
REVERT: B   93 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7364 (mp10)
REVERT: C   64 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8208 (tt0)
REVERT: G   36 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8597 (mtpp)
REVERT: H   98 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9128 (mm)
REVERT: K    1 MET cc_start: 0.6267 (tmm) cc_final: 0.5994 (tmm)
  outliers start: 15
  outliers final: 11
  residues processed: 132
  average time/residue: 0.3432
  time to fit residues: 60.3325
Evaluate side-chains
  141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.117389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.084164 restraints weight = 21716.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.18
r_work: 0.2846 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  13842  Z= 0.254
  Angle     :  0.559   5.600  20050  Z= 0.340
  Chirality :  0.036   0.133   2291
  Planarity :  0.004   0.038   1450
  Dihedral  : 30.347 176.442   4342
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.73 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.30), residues: 800
  helix:  2.76 (0.22), residues: 542
  sheet:  2.21 (1.16), residues: 23
  loop : -0.49 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  39 
 PHE   0.009   0.002   PHE F  61 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.002   0.000   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06611 (  828)
  hydrogen bonds       : angle       2.91013 ( 2046)
  covalent geometry    : bond        0.00571 (13842)
  covalent geometry    : angle       0.55932 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.880 
Fit side-chains
REVERT: B   93 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7385 (mp10)
REVERT: C   64 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8214 (tt0)
REVERT: E  131 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8912 (mtp85)
REVERT: G   36 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8598 (mtpp)
REVERT: G   73 ASN cc_start: 0.8257 (t0) cc_final: 0.7726 (t0)
REVERT: H   98 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9126 (mm)
  outliers start: 16
  outliers final: 9
  residues processed: 133
  average time/residue: 0.3434
  time to fit residues: 60.1863
Evaluate side-chains
  140 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 106 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 86 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
K  41 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.117539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.084238 restraints weight = 21585.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.26
r_work: 0.2809 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13842  Z= 0.241
  Angle     :  0.561   7.667  20050  Z= 0.340
  Chirality :  0.035   0.135   2291
  Planarity :  0.004   0.038   1450
  Dihedral  : 30.346 176.858   4342
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.88 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.30), residues: 800
  helix:  2.75 (0.22), residues: 542
  sheet:  1.40 (1.61), residues: 12
  loop : -0.43 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  39 
 PHE   0.009   0.002   PHE F  61 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.002   0.000   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06392 (  828)
  hydrogen bonds       : angle       2.90788 ( 2046)
  covalent geometry    : bond        0.00541 (13842)
  covalent geometry    : angle       0.56087 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7896 (mtp180)
REVERT: B   93 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7329 (mp10)
REVERT: C   64 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7988 (tt0)
REVERT: E  131 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (mtp85)
REVERT: G   36 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8513 (mtpp)
REVERT: G   73 ASN cc_start: 0.8165 (t0) cc_final: 0.7642 (t0)
REVERT: H   98 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9099 (mm)
  outliers start: 19
  outliers final: 11
  residues processed: 135
  average time/residue: 0.4300
  time to fit residues: 77.7958
Evaluate side-chains
  144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   66 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 106 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.117994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.084759 restraints weight = 21628.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.14
r_work: 0.2871 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13842  Z= 0.186
  Angle     :  0.550   6.404  20050  Z= 0.334
  Chirality :  0.033   0.125   2291
  Planarity :  0.004   0.038   1450
  Dihedral  : 30.355 177.016   4342
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.31 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.30), residues: 800
  helix:  2.81 (0.22), residues: 542
  sheet:  1.38 (1.61), residues: 12
  loop : -0.39 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS K  68 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.001   0.000   ARG E  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06104 (  828)
  hydrogen bonds       : angle       2.89926 ( 2046)
  covalent geometry    : bond        0.00400 (13842)
  covalent geometry    : angle       0.54954 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8012 (mtp180)
REVERT: B   93 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7358 (mp10)
REVERT: C   64 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8175 (tt0)
REVERT: E  131 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8882 (mtp85)
REVERT: G   36 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8618 (mtpp)
REVERT: G   73 ASN cc_start: 0.8209 (t0) cc_final: 0.7706 (t0)
REVERT: H   98 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9100 (mm)
  outliers start: 18
  outliers final: 11
  residues processed: 136
  average time/residue: 0.3586
  time to fit residues: 64.4434
Evaluate side-chains
  143 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 107 optimal weight:   20.0000
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.117863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.084468 restraints weight = 21535.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.25
r_work: 0.2828 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13842  Z= 0.225
  Angle     :  0.550   7.114  20050  Z= 0.334
  Chirality :  0.035   0.126   2291
  Planarity :  0.004   0.037   1450
  Dihedral  : 30.326 177.578   4342
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.31 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.30), residues: 800
  helix:  2.81 (0.22), residues: 542
  sheet:  1.31 (1.59), residues: 12
  loop : -0.38 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.002   0.000   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06063 (  828)
  hydrogen bonds       : angle       2.84935 ( 2046)
  covalent geometry    : bond        0.00501 (13842)
  covalent geometry    : angle       0.54963 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.341 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8041 (mtp180)
REVERT: B   93 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7364 (mp10)
REVERT: C   64 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8247 (tt0)
REVERT: E  131 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8924 (mtp85)
REVERT: G   36 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8615 (mtpp)
REVERT: G   73 ASN cc_start: 0.8231 (t0) cc_final: 0.7732 (t0)
REVERT: H   98 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9094 (mm)
REVERT: K    1 MET cc_start: 0.6460 (tmm) cc_final: 0.5882 (tmm)
  outliers start: 18
  outliers final: 11
  residues processed: 137
  average time/residue: 0.3838
  time to fit residues: 70.4211
Evaluate side-chains
  144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 106 optimal weight:   30.0000
   chunk 36 optimal weight:    0.0040
   chunk 64 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.118573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.085420 restraints weight = 21445.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.15
r_work: 0.2890 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8891
moved from start:          0.0973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13842  Z= 0.163
  Angle     :  0.543   6.887  20050  Z= 0.331
  Chirality :  0.033   0.146   2291
  Planarity :  0.004   0.038   1450
  Dihedral  : 30.336 177.726   4342
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.31 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.90 (0.30), residues: 800
  helix:  2.89 (0.22), residues: 542
  sheet:  1.29 (1.58), residues: 12
  loop : -0.33 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.002   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05572 (  828)
  hydrogen bonds       : angle       2.86299 ( 2046)
  covalent geometry    : bond        0.00341 (13842)
  covalent geometry    : angle       0.54291 (20050)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7966 (mtp180)
REVERT: B   93 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7321 (mp10)
REVERT: C   64 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8163 (tt0)
REVERT: E  131 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8883 (mtp85)
REVERT: G   36 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8602 (mtpp)
REVERT: G   73 ASN cc_start: 0.8155 (t0) cc_final: 0.7670 (t0)
REVERT: H   98 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9075 (mm)
REVERT: K    1 MET cc_start: 0.6532 (tmm) cc_final: 0.5981 (tmm)
  outliers start: 18
  outliers final: 10
  residues processed: 136
  average time/residue: 0.3656
  time to fit residues: 65.6227
Evaluate side-chains
  143 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   66 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0770
   chunk 98 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   overall best weight:    2.1544

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

Flipped N/Q/H residues before XYZ refinement:
D  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.117608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.084338 restraints weight = 21641.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.15
r_work: 0.2864 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8917
moved from start:          0.1049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13842  Z= 0.237
  Angle     :  0.555   6.682  20050  Z= 0.336
  Chirality :  0.035   0.127   2291
  Planarity :  0.004   0.038   1450
  Dihedral  : 30.295 177.085   4342
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.60 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.30), residues: 800
  helix:  2.85 (0.22), residues: 542
  sheet:  1.24 (1.58), residues: 12
  loop : -0.42 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.002   PHE F  61 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.005   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06334 (  828)
  hydrogen bonds       : angle       2.86736 ( 2046)
  covalent geometry    : bond        0.00530 (13842)
  covalent geometry    : angle       0.55491 (20050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7115.26 seconds
wall clock time: 123 minutes 58.14 seconds (7438.14 seconds total)