Starting phenix.real_space_refine
on Mon May 19 11:38:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u14_41801/05_2025/8u14_41801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u14_41801/05_2025/8u14_41801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u14_41801/05_2025/8u14_41801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u14_41801/05_2025/8u14_41801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u14_41801/05_2025/8u14_41801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u14_41801/05_2025/8u14_41801.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     293      5.49       5
     S      32      5.16       5
     C    7885      2.51       5
     N    2608      2.21       5
     O    3175      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13995
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "D"
      Number of atoms: 751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 751
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3010
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 706
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 88, 702
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 81}
      Conformer: "B"
        Number of residues, atoms: 88, 702
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 81}
          bond proxies already assigned to first conformer: 713
    Chain: "L"
      Number of atoms: 1176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1176
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "G"
      Number of atoms: 843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 843
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  10611  SG  CYS K  31      77.501  68.587  45.284  1.00155.98           S
  ATOM  10761  SG  CYS K  51      77.762  71.763  47.414  1.00157.25           S
  ATOM  10785  SG  CYS K  54      76.542  71.999  43.785  1.00157.66           S
  ATOM  10502  SG  CYS K  16      86.876  72.181  56.653  1.00201.51           S
  ATOM  10520  SG  CYS K  19      87.004  73.675  59.834  1.00219.51           S
  ATOM  10650  SG  CYS K  36      84.987  70.188  59.204  1.00192.64           S
  ATOM  10672  SG  CYS K  39      83.453  73.315  58.539  1.00199.41           S

  Time building chain proxies: 9.01, per 1000 atoms: 0.64
  Number of scatterers: 13995
  At special positions: 0
  Unit cell: (107.898, 126.395, 118.174, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      32     16.00
     P     293     15.00
     O    3175      8.00
     N    2608      7.00
     C    7885      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 3.60
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
      Number of angles added : 9


  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 8 sheets defined
      65.5% alpha, 3.3% beta
      140 base pairs and 241 stacking pairs defined.
    Time for finding SS restraints: 6.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.702A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.768A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.639A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.799A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.653A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    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 41
      removed outlier: 3.528A  pdb=" N   GLY F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.365A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.514A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
    Processing helix  chain 'K' and resid 36 through 45
      removed outlier: 3.664A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 4.642A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 92
      removed outlier: 3.935A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.983A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.535A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 147
      removed outlier: 3.700A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA L 146 " --> pdb=" O   THR L 142 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   MET L 147 " --> pdb=" O   GLN L 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.395A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.898A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 74
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 92 through 98
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.634A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.214A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.600A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'H' and resid 53 through 54
      removed outlier: 7.393A  pdb=" N   GLY H  53 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'H' and resid 88 through 89
    Processing sheet with id=AA7, first strand: chain 'K' and resid 27 through 28
      removed outlier: 3.555A  pdb=" N   VAL K  27 " --> pdb=" O   LEU K  35 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'L' and resid 21 through 25

    486 hydrogen bonds defined for protein.
    1442 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      358 hydrogen bonds
      712 hydrogen bond angles
      0 basepair planarities
      140 basepair parallelities
      241 stacking parallelities
  Total time for adding SS restraints: 5.07

  Time building geometry restraints manager: 4.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3398
        1.34 -     1.46: 4244
        1.46 -     1.58: 6583
        1.58 -     1.70: 584
        1.70 -     1.82: 46
  Bond restraints: 14855
  Sorted by residual:
  bond pdb=" C   HIS H  49 "
       pdb=" O   HIS H  49 "
    ideal  model  delta    sigma   weight residual
    1.249  1.237  0.012 8.50e-03 1.38e+04 1.91e+00
  bond pdb=" CB  LYS B  59 "
       pdb=" CG  LYS B  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.63e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.40e+00
  bond pdb=" N   ASP B  24 "
       pdb=" CA  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.460  1.476 -0.017 1.42e-02 4.96e+03 1.35e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.32e+00
  ... (remaining 14850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 20629
        1.65 -     3.29: 625
        3.29 -     4.94: 58
        4.94 -     6.59: 16
        6.59 -     8.23: 6
  Bond angle restraints: 21334
  Sorted by residual:
  angle pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
      ideal   model   delta    sigma   weight residual
     113.53  108.56    4.97 9.80e-01 1.04e+00 2.57e+01
  angle pdb=" N   GLU F  63 "
        pdb=" CA  GLU F  63 "
        pdb=" CB  GLU F  63 "
      ideal   model   delta    sigma   weight residual
     110.39  116.07   -5.68 1.66e+00 3.63e-01 1.17e+01
  angle pdb=" CA  GLU F  63 "
        pdb=" CB  GLU F  63 "
        pdb=" CG  GLU F  63 "
      ideal   model   delta    sigma   weight residual
     114.10  120.81   -6.71 2.00e+00 2.50e-01 1.13e+01
  angle pdb=" CB  LYS B  59 "
        pdb=" CG  LYS B  59 "
        pdb=" CD  LYS B  59 "
      ideal   model   delta    sigma   weight residual
     111.30  118.47   -7.17 2.30e+00 1.89e-01 9.73e+00
  angle pdb=" N   ARG B  36 "
        pdb=" CA  ARG B  36 "
        pdb=" CB  ARG B  36 "
      ideal   model   delta    sigma   weight residual
     110.28  114.90   -4.62 1.55e+00 4.16e-01 8.88e+00
  ... (remaining 21329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.61: 6645
       31.61 -    63.22: 1529
       63.22 -    94.84: 42
       94.84 -   126.45: 0
      126.45 -   158.06: 2
  Dihedral angle restraints: 8218
    sinusoidal: 5288
      harmonic: 2930
  Sorted by residual:
  dihedral pdb=" CA  ASN B  25 "
           pdb=" C   ASN B  25 "
           pdb=" N   ILE B  26 "
           pdb=" CA  ILE B  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  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   61.94  158.06     1      3.50e+01 8.16e-04 1.51e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   65.92  154.08     1      3.50e+01 8.16e-04 1.49e+01
  ... (remaining 8215 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1787
       0.034 -    0.069: 477
       0.069 -    0.103: 120
       0.103 -    0.138: 29
       0.138 -    0.172: 5
  Chirality restraints: 2418
  Sorted by residual:
  chirality pdb=" CA  GLU F  63 "
            pdb=" N   GLU F  63 "
            pdb=" C   GLU F  63 "
            pdb=" CB  GLU F  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.39e-01
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  GLN E 125 "
            pdb=" N   GLN E 125 "
            pdb=" C   GLN E 125 "
            pdb=" CB  GLN E 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 2415 not shown)

  Planarity restraints: 1692
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "    0.024 2.00e-02 2.50e+03   1.04e-02 2.98e+00
        pdb=" N9   DA I -35 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  59 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.77e+00
        pdb=" C   LYS F  59 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS F  59 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL F  60 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  73 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" CD  GLU A  73 "    0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  73 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  73 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1689 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 466
        2.68 -     3.23: 13143
        3.23 -     3.79: 27192
        3.79 -     4.34: 32816
        4.34 -     4.90: 46740
  Nonbonded interactions: 120357
  Sorted by model distance:
  nonbonded pdb=" O   ARG K  63 "
            pdb=" NH1 ARG K  67 "
     model   vdw
     2.124 3.120
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.150 2.496
  nonbonded pdb=" OE1 GLN D  95 "
            pdb=" OH  TYR C  50 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" NE2 HIS B  75 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OE2 GLU H 105 "
            pdb=" NH1 ARG K  67 "
     model   vdw
     2.223 3.120
  ... (remaining 120352 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 119)
}
ncs_group {
  reference = (chain 'D' and resid 31 through 123)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.130
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     40.410
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.060
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
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   0.040  14865  Z= 0.159
  Angle     :  0.665  12.911  21349  Z= 0.372
  Chirality :  0.035   0.172   2418
  Planarity :  0.004   0.041   1690
  Dihedral  : 26.360 158.059   6320
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.27), residues: 987
  helix:  1.25 (0.21), residues: 623
  sheet:  0.72 (0.98), residues: 24
  loop : -1.10 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K  61 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.017   0.001   PHE E  78 
 TYR   0.024   0.001   TYR F  88 
 ARG   0.016   0.001   ARG B  36 

Details of bonding type rmsd
  link_TRANS           : bond        0.00188 (    2)
  link_TRANS           : angle       0.84845 (    6)
  hydrogen bonds       : bond        0.10380 (  844)
  hydrogen bonds       : angle       4.37418 ( 2154)
  metal coordination   : bond        0.00526 (    8)
  metal coordination   : angle       7.88243 (    9)
  covalent geometry    : bond        0.00335 (14855)
  covalent geometry    : angle       0.64522 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 354
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.8750 (m-30) cc_final: 0.8495 (m-30)
REVERT: A  125 GLN cc_start: 0.8605 (mp10) cc_final: 0.7989 (mp10)
REVERT: D   59 MET cc_start: 0.8760 (tpt) cc_final: 0.8526 (tpt)
REVERT: E   73 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8008 (mt-10)
REVERT: E   77 ASP cc_start: 0.8106 (m-30) cc_final: 0.7873 (m-30)
REVERT: E  120 MET cc_start: 0.8851 (mmm) cc_final: 0.8432 (mmm)
REVERT: F   31 LYS cc_start: 0.9471 (tttm) cc_final: 0.9057 (tptm)
REVERT: F   64 ASN cc_start: 0.8753 (m-40) cc_final: 0.8430 (m110)
REVERT: H   47 GLN cc_start: 0.8800 (tt0) cc_final: 0.8495 (tm-30)
REVERT: H   48 VAL cc_start: 0.9346 (p) cc_final: 0.9145 (p)
REVERT: H   71 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: H   85 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9034 (mtmm)
REVERT: K   18 ILE cc_start: 0.8706 (mm) cc_final: 0.8483 (mm)
REVERT: K   41 GLN cc_start: 0.9313 (mt0) cc_final: 0.8888 (mp10)
REVERT: C   56 GLU cc_start: 0.9069 (tp30) cc_final: 0.8812 (tp30)
REVERT: C   90 ASP cc_start: 0.8551 (t70) cc_final: 0.8319 (t0)
REVERT: G   92 GLU cc_start: 0.7885 (pt0) cc_final: 0.7273 (pt0)
REVERT: G  104 GLN cc_start: 0.8553 (tt0) cc_final: 0.7766 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 354
  average time/residue: 0.3179
  time to fit residues: 152.1874
Evaluate side-chains
  279 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 93 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 96 optimal weight:   20.0000
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.081680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.058240 restraints weight = 76087.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.060090 restraints weight = 35992.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.061166 restraints weight = 23464.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14865  Z= 0.196
  Angle     :  0.677  14.110  21349  Z= 0.374
  Chirality :  0.038   0.177   2418
  Planarity :  0.005   0.035   1690
  Dihedral  : 29.614 156.743   4321
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.07 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 987
  helix:  1.32 (0.20), residues: 631
  sheet:  0.31 (0.98), residues: 24
  loop : -1.23 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP L  33 
 HIS   0.006   0.001   HIS K  65 
 PHE   0.018   0.002   PHE A 104 
 TYR   0.027   0.002   TYR B  88 
 ARG   0.006   0.001   ARG L 136 

Details of bonding type rmsd
  link_TRANS           : bond        0.00062 (    2)
  link_TRANS           : angle       0.18495 (    6)
  hydrogen bonds       : bond        0.04685 (  844)
  hydrogen bonds       : angle       3.84715 ( 2154)
  metal coordination   : bond        0.01162 (    8)
  metal coordination   : angle       8.25547 (    9)
  covalent geometry    : bond        0.00432 (14855)
  covalent geometry    : angle       0.65611 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 303
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.8991 (tppp) cc_final: 0.8773 (tppp)
REVERT: A  125 GLN cc_start: 0.8448 (mp10) cc_final: 0.8092 (mp10)
REVERT: B   84 MET cc_start: 0.9289 (tpp) cc_final: 0.8732 (tpp)
REVERT: D   33 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8104 (tpp80)
REVERT: D   79 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8423 (ttm110)
REVERT: D   95 GLN cc_start: 0.9046 (tp40) cc_final: 0.8536 (tp40)
REVERT: E   77 ASP cc_start: 0.8263 (m-30) cc_final: 0.7999 (m-30)
REVERT: E  120 MET cc_start: 0.8785 (mmm) cc_final: 0.8367 (mmm)
REVERT: F   84 MET cc_start: 0.8126 (tpp) cc_final: 0.7824 (tpp)
REVERT: F   92 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8276 (ttp80)
REVERT: H   47 GLN cc_start: 0.8842 (tt0) cc_final: 0.8494 (tm-30)
REVERT: H   71 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8459 (tm-30)
REVERT: K   86 ARG cc_start: 0.9405 (pmt170) cc_final: 0.9063 (pmt170)
REVERT: L   63 LYS cc_start: 0.7664 (tptt) cc_final: 0.7367 (tppt)
REVERT: C   73 ASN cc_start: 0.9497 (t0) cc_final: 0.9247 (t0)
REVERT: C   90 ASP cc_start: 0.8555 (t70) cc_final: 0.8203 (t0)
REVERT: G  104 GLN cc_start: 0.8686 (tt0) cc_final: 0.7866 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 310
  average time/residue: 0.3088
  time to fit residues: 130.5142
Evaluate side-chains
  294 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 285
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   94 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    0.1980
   chunk 102 optimal weight:    0.9980
   chunk 121 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 ASN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.082477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.060009 restraints weight = 67605.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.061721 restraints weight = 32449.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.062877 restraints weight = 21199.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14865  Z= 0.160
  Angle     :  0.651  12.209  21349  Z= 0.360
  Chirality :  0.037   0.175   2418
  Planarity :  0.004   0.036   1690
  Dihedral  : 29.611 156.401   4321
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.40 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 987
  helix:  1.43 (0.20), residues: 629
  sheet:  0.38 (1.01), residues: 24
  loop : -1.28 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP K  61 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.013   0.001   PHE A 104 
 TYR   0.032   0.002   TYR B  88 
 ARG   0.008   0.001   ARG K  67 

Details of bonding type rmsd
  link_TRANS           : bond        0.00023 (    2)
  link_TRANS           : angle       0.19729 (    6)
  hydrogen bonds       : bond        0.04158 (  844)
  hydrogen bonds       : angle       3.68654 ( 2154)
  metal coordination   : bond        0.00616 (    8)
  metal coordination   : angle       7.25588 (    9)
  covalent geometry    : bond        0.00348 (14855)
  covalent geometry    : angle       0.63351 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 307
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8847 (tmm-80) cc_final: 0.8647 (tmm-80)
REVERT: A   64 LYS cc_start: 0.8834 (tppp) cc_final: 0.8514 (tppp)
REVERT: A  106 ASP cc_start: 0.8844 (m-30) cc_final: 0.8490 (m-30)
REVERT: A  125 GLN cc_start: 0.8355 (mt0) cc_final: 0.8069 (mp10)
REVERT: B   54 THR cc_start: 0.9429 (m) cc_final: 0.9174 (p)
REVERT: D   33 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8174 (tpp80)
REVERT: D   79 ARG cc_start: 0.8701 (ttm110) cc_final: 0.8307 (ttm110)
REVERT: D   95 GLN cc_start: 0.9061 (tp40) cc_final: 0.8589 (tp40)
REVERT: E   73 GLU cc_start: 0.8738 (tt0) cc_final: 0.8432 (tt0)
REVERT: E   77 ASP cc_start: 0.8275 (m-30) cc_final: 0.8033 (m-30)
REVERT: E   90 MET cc_start: 0.8128 (mmt) cc_final: 0.7769 (mmp)
REVERT: E  120 MET cc_start: 0.8938 (mmm) cc_final: 0.8438 (mmm)
REVERT: F   39 ARG cc_start: 0.9303 (tpp80) cc_final: 0.8650 (mmm-85)
REVERT: F   84 MET cc_start: 0.8095 (tpp) cc_final: 0.7764 (tpp)
REVERT: F   92 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8268 (ttp80)
REVERT: H   47 GLN cc_start: 0.8804 (tt0) cc_final: 0.8487 (tm-30)
REVERT: H   71 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8537 (tm-30)
REVERT: H   85 LYS cc_start: 0.9345 (mtmm) cc_final: 0.9143 (mtmm)
REVERT: H   93 GLU cc_start: 0.8925 (mp0) cc_final: 0.8665 (mp0)
REVERT: H  116 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8732 (mmtp)
REVERT: K   65 HIS cc_start: 0.8748 (m90) cc_final: 0.8186 (m90)
REVERT: L   63 LYS cc_start: 0.7619 (tptt) cc_final: 0.7262 (tppt)
REVERT: C   73 ASN cc_start: 0.9435 (t0) cc_final: 0.9163 (t0)
REVERT: C   90 ASP cc_start: 0.8546 (t70) cc_final: 0.8180 (t0)
REVERT: G   57 TYR cc_start: 0.8703 (t80) cc_final: 0.8490 (t80)
REVERT: G   84 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8531 (tp-100)
REVERT: G   90 ASP cc_start: 0.8606 (t70) cc_final: 0.8145 (t0)
REVERT: G  104 GLN cc_start: 0.8697 (tt0) cc_final: 0.7794 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 317
  average time/residue: 0.2920
  time to fit residues: 127.6782
Evaluate side-chains
  301 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 284
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   94 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 119 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 92 optimal weight:   30.0000
   chunk 60 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 ASN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.081192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.056846 restraints weight = 91889.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.058733 restraints weight = 40506.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.059944 restraints weight = 25446.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14865  Z= 0.196
  Angle     :  0.660  12.066  21349  Z= 0.365
  Chirality :  0.037   0.173   2418
  Planarity :  0.004   0.035   1690
  Dihedral  : 29.735 155.589   4321
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 22.73 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.27), residues: 987
  helix:  1.51 (0.21), residues: 630
  sheet:  0.50 (1.07), residues: 24
  loop : -1.20 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP K  61 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.039   0.002   TYR B  88 
 ARG   0.006   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00100 (    2)
  link_TRANS           : angle       0.23323 (    6)
  hydrogen bonds       : bond        0.04550 (  844)
  hydrogen bonds       : angle       3.68494 ( 2154)
  metal coordination   : bond        0.01396 (    8)
  metal coordination   : angle       7.58969 (    9)
  covalent geometry    : bond        0.00436 (14855)
  covalent geometry    : angle       0.64119 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 295
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   33 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8185 (tpp80)
REVERT: E   73 GLU cc_start: 0.8712 (tt0) cc_final: 0.8433 (tt0)
REVERT: E   77 ASP cc_start: 0.8251 (m-30) cc_final: 0.8028 (m-30)
REVERT: E   90 MET cc_start: 0.8213 (mmt) cc_final: 0.7843 (mmp)
REVERT: E  120 MET cc_start: 0.8946 (mmm) cc_final: 0.8405 (mmm)
REVERT: F   84 MET cc_start: 0.8182 (tpp) cc_final: 0.7970 (tpp)
REVERT: F   92 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8349 (ttp80)
REVERT: H   47 GLN cc_start: 0.8799 (tt0) cc_final: 0.8496 (tm-30)
REVERT: H  116 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8723 (mmtp)
REVERT: K   68 ARG cc_start: 0.6947 (mpp-170) cc_final: 0.6330 (mpp80)
REVERT: L   63 LYS cc_start: 0.7526 (tptt) cc_final: 0.7197 (tppt)
REVERT: C   73 ASN cc_start: 0.9396 (t0) cc_final: 0.9101 (t0)
REVERT: C   90 ASP cc_start: 0.8554 (t70) cc_final: 0.8203 (t0)
REVERT: G   84 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8495 (tp-100)
REVERT: G   90 ASP cc_start: 0.8577 (t70) cc_final: 0.8365 (t0)
REVERT: G  104 GLN cc_start: 0.8712 (tt0) cc_final: 0.7764 (tm-30)
  outliers start: 34
  outliers final: 26
  residues processed: 307
  average time/residue: 0.3040
  time to fit residues: 128.1350
Evaluate side-chains
  305 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 279
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   72 VAL
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   54 ILE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   94 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 122 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 ASN
G  38 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.082363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.059062 restraints weight = 63289.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.060601 restraints weight = 32997.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.061637 restraints weight = 22648.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  14865  Z= 0.161
  Angle     :  0.653  11.958  21349  Z= 0.361
  Chirality :  0.037   0.182   2418
  Planarity :  0.004   0.037   1690
  Dihedral  : 29.701 155.114   4321
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 24.24 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.27), residues: 987
  helix:  1.48 (0.20), residues: 626
  sheet:  0.47 (1.08), residues: 24
  loop : -1.18 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.049   0.002   TYR B  88 
 ARG   0.008   0.000   ARG F  39 

Details of bonding type rmsd
  link_TRANS           : bond        0.00040 (    2)
  link_TRANS           : angle       0.14187 (    6)
  hydrogen bonds       : bond        0.04007 (  844)
  hydrogen bonds       : angle       3.63238 ( 2154)
  metal coordination   : bond        0.00730 (    8)
  metal coordination   : angle       7.05819 (    9)
  covalent geometry    : bond        0.00354 (14855)
  covalent geometry    : angle       0.63681 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 295
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8489 (pp20) cc_final: 0.7751 (pp20)
REVERT: A   53 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8256 (tmm-80)
REVERT: A   76 GLN cc_start: 0.8869 (pp30) cc_final: 0.8658 (pp30)
REVERT: D   79 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8335 (ttm110)
REVERT: E   73 GLU cc_start: 0.8719 (tt0) cc_final: 0.8387 (tt0)
REVERT: E   77 ASP cc_start: 0.8128 (m-30) cc_final: 0.7888 (m-30)
REVERT: E   90 MET cc_start: 0.8153 (mmt) cc_final: 0.7848 (mmp)
REVERT: E  120 MET cc_start: 0.8933 (mmm) cc_final: 0.8316 (mmm)
REVERT: F   84 MET cc_start: 0.8104 (tpp) cc_final: 0.7870 (tpp)
REVERT: F   92 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8310 (ttp80)
REVERT: H   47 GLN cc_start: 0.8765 (tt0) cc_final: 0.8487 (tm-30)
REVERT: H   93 GLU cc_start: 0.8960 (mp0) cc_final: 0.8681 (mp0)
REVERT: H  116 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8682 (mmtp)
REVERT: K   64 TYR cc_start: 0.8400 (t80) cc_final: 0.8131 (t80)
REVERT: L   32 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.8126 (m-70)
REVERT: C   73 ASN cc_start: 0.9337 (t0) cc_final: 0.9035 (t0)
REVERT: C   90 ASP cc_start: 0.8525 (t70) cc_final: 0.8180 (t0)
REVERT: G   57 TYR cc_start: 0.8704 (t80) cc_final: 0.8488 (t80)
REVERT: G   84 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8748 (tp-100)
  outliers start: 33
  outliers final: 27
  residues processed: 307
  average time/residue: 0.3041
  time to fit residues: 128.4250
Evaluate side-chains
  314 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 286
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   70 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   72 VAL
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   94 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 92 optimal weight:   30.0000
   chunk 86 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 117 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
C  94 ASN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.080461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.056053 restraints weight = 87747.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.057883 restraints weight = 39716.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.059052 restraints weight = 25429.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  14865  Z= 0.213
  Angle     :  0.688  13.215  21349  Z= 0.379
  Chirality :  0.038   0.190   2418
  Planarity :  0.004   0.035   1690
  Dihedral  : 29.852 154.738   4321
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 25.29 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.26), residues: 987
  helix:  1.44 (0.20), residues: 626
  sheet:  0.31 (1.05), residues: 24
  loop : -1.18 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP K  61 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.053   0.002   TYR B  88 
 ARG   0.010   0.001   ARG K  67 

Details of bonding type rmsd
  link_TRANS           : bond        0.00106 (    2)
  link_TRANS           : angle       0.25615 (    6)
  hydrogen bonds       : bond        0.04817 (  844)
  hydrogen bonds       : angle       3.72483 ( 2154)
  metal coordination   : bond        0.01764 (    8)
  metal coordination   : angle       7.04498 (    9)
  covalent geometry    : bond        0.00478 (14855)
  covalent geometry    : angle       0.67325 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 296
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8477 (pp20) cc_final: 0.7618 (pp20)
REVERT: A   53 ARG cc_start: 0.8880 (tmm-80) cc_final: 0.8225 (tmm-80)
REVERT: A   76 GLN cc_start: 0.8953 (pp30) cc_final: 0.8744 (pp30)
REVERT: E   73 GLU cc_start: 0.8742 (tt0) cc_final: 0.8439 (tt0)
REVERT: E   77 ASP cc_start: 0.8187 (m-30) cc_final: 0.7971 (m-30)
REVERT: E   90 MET cc_start: 0.8088 (mmt) cc_final: 0.7775 (mmp)
REVERT: E  120 MET cc_start: 0.8967 (mmm) cc_final: 0.8327 (mmm)
REVERT: E  126 LEU cc_start: 0.9614 (tt) cc_final: 0.9394 (tp)
REVERT: F   84 MET cc_start: 0.8217 (tpp) cc_final: 0.7938 (tpp)
REVERT: F   92 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8270 (ttp80)
REVERT: H   47 GLN cc_start: 0.8772 (tt0) cc_final: 0.8504 (tm-30)
REVERT: H   93 GLU cc_start: 0.8946 (mp0) cc_final: 0.8642 (mp0)
REVERT: H  116 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8681 (mmtp)
REVERT: K   64 TYR cc_start: 0.8418 (t80) cc_final: 0.8168 (t80)
REVERT: L   32 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8186 (m-70)
REVERT: L   63 LYS cc_start: 0.7486 (tptt) cc_final: 0.7159 (tppt)
REVERT: C   73 ASN cc_start: 0.9363 (t0) cc_final: 0.9065 (t0)
REVERT: C   90 ASP cc_start: 0.8543 (t70) cc_final: 0.8221 (t0)
REVERT: G   91 GLU cc_start: 0.8371 (pp20) cc_final: 0.8054 (pp20)
  outliers start: 36
  outliers final: 30
  residues processed: 310
  average time/residue: 0.3016
  time to fit residues: 128.5274
Evaluate side-chains
  316 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 285
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   72 VAL
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   94 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 103 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 111 optimal weight:    0.3980
   chunk 73 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
E  68 GLN
H  49 HIS
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 ASN
G  38 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.082735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.058711 restraints weight = 76188.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.060469 restraints weight = 36304.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.061625 restraints weight = 23670.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14865  Z= 0.161
  Angle     :  0.689  13.066  21349  Z= 0.377
  Chirality :  0.037   0.213   2418
  Planarity :  0.004   0.038   1690
  Dihedral  : 29.764 154.509   4321
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.46 %
    Favored  : 69.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 987
  helix:  1.37 (0.20), residues: 628
  sheet:  0.61 (1.09), residues: 24
  loop : -1.11 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.016   0.001   PHE H  70 
 TYR   0.044   0.002   TYR B  88 
 ARG   0.008   0.001   ARG K  67 

Details of bonding type rmsd
  link_TRANS           : bond        0.00010 (    2)
  link_TRANS           : angle       0.13542 (    6)
  hydrogen bonds       : bond        0.04028 (  844)
  hydrogen bonds       : angle       3.61969 ( 2154)
  metal coordination   : bond        0.00630 (    8)
  metal coordination   : angle       6.77813 (    9)
  covalent geometry    : bond        0.00357 (14855)
  covalent geometry    : angle       0.67494 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 294
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9126 (tppp) cc_final: 0.8771 (tppp)
REVERT: A   76 GLN cc_start: 0.8883 (pp30) cc_final: 0.8658 (pp30)
REVERT: B   88 TYR cc_start: 0.8771 (m-80) cc_final: 0.8555 (m-80)
REVERT: D   83 TYR cc_start: 0.7750 (m-10) cc_final: 0.7541 (m-10)
REVERT: E   90 MET cc_start: 0.8077 (mmt) cc_final: 0.7765 (mmp)
REVERT: E  120 MET cc_start: 0.8984 (mmm) cc_final: 0.8391 (mmm)
REVERT: F   35 ARG cc_start: 0.9421 (ttp80) cc_final: 0.9213 (ttm110)
REVERT: F   84 MET cc_start: 0.8234 (tpp) cc_final: 0.7917 (tpp)
REVERT: F   92 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8394 (ttp80)
REVERT: H   34 LYS cc_start: 0.9002 (tptp) cc_final: 0.8756 (tptt)
REVERT: H   47 GLN cc_start: 0.8734 (tt0) cc_final: 0.8499 (tm-30)
REVERT: H   93 GLU cc_start: 0.8957 (mp0) cc_final: 0.8643 (mp0)
REVERT: K   63 ARG cc_start: 0.8286 (ptm-80) cc_final: 0.8062 (ptm-80)
REVERT: L   32 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8179 (m-70)
REVERT: L   63 LYS cc_start: 0.7393 (tptt) cc_final: 0.7061 (tppt)
REVERT: C   73 ASN cc_start: 0.9327 (t0) cc_final: 0.9015 (t0)
REVERT: C   90 ASP cc_start: 0.8575 (t70) cc_final: 0.8228 (t0)
REVERT: G   57 TYR cc_start: 0.8659 (t80) cc_final: 0.8428 (t80)
REVERT: G   92 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7395 (pm20)
  outliers start: 39
  outliers final: 31
  residues processed: 308
  average time/residue: 0.2922
  time to fit residues: 124.1876
Evaluate side-chains
  310 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 277
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   72 VAL
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   94 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 88 optimal weight:    0.8980
   chunk 120 optimal weight:    4.9990
   chunk 119 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0010
   chunk 55 optimal weight:    6.9990
   chunk 111 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 118 optimal weight:    0.1980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
E  68 GLN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  77 ASN
G  38 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.083450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.059579 restraints weight = 75886.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.061249 restraints weight = 36040.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.062420 restraints weight = 23612.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14865  Z= 0.160
  Angle     :  0.693  13.761  21349  Z= 0.380
  Chirality :  0.037   0.197   2418
  Planarity :  0.004   0.039   1690
  Dihedral  : 29.724 155.775   4321
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 26.69 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 987
  helix:  1.33 (0.20), residues: 628
  sheet:  0.58 (0.96), residues: 29
  loop : -1.08 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP K  61 
 HIS   0.010   0.001   HIS L  75 
 PHE   0.014   0.001   PHE H  70 
 TYR   0.031   0.002   TYR B  88 
 ARG   0.008   0.001   ARG K  67 

Details of bonding type rmsd
  link_TRANS           : bond        0.00020 (    2)
  link_TRANS           : angle       0.06175 (    6)
  hydrogen bonds       : bond        0.04037 (  844)
  hydrogen bonds       : angle       3.60794 ( 2154)
  metal coordination   : bond        0.00563 (    8)
  metal coordination   : angle       6.64125 (    9)
  covalent geometry    : bond        0.00353 (14855)
  covalent geometry    : angle       0.68016 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 295
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8848 (tmm-80) cc_final: 0.8221 (tmm-80)
REVERT: A   64 LYS cc_start: 0.9109 (tppp) cc_final: 0.8786 (tppp)
REVERT: A   76 GLN cc_start: 0.8889 (pp30) cc_final: 0.8655 (pp30)
REVERT: B   54 THR cc_start: 0.9403 (m) cc_final: 0.9177 (p)
REVERT: B   59 LYS cc_start: 0.9114 (tppt) cc_final: 0.8358 (tptp)
REVERT: B   88 TYR cc_start: 0.8604 (m-80) cc_final: 0.8287 (m-80)
REVERT: D   59 MET cc_start: 0.8720 (tpt) cc_final: 0.8500 (tpt)
REVERT: D   83 TYR cc_start: 0.7692 (m-10) cc_final: 0.7149 (m-10)
REVERT: D  105 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7980 (tm-30)
REVERT: D  109 HIS cc_start: 0.8073 (m-70) cc_final: 0.6770 (m170)
REVERT: E   90 MET cc_start: 0.8024 (mmt) cc_final: 0.7718 (mmp)
REVERT: E  108 ASN cc_start: 0.9120 (t0) cc_final: 0.8747 (t0)
REVERT: E  120 MET cc_start: 0.8980 (mmm) cc_final: 0.8407 (mmm)
REVERT: F   67 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7731 (tpm170)
REVERT: F   84 MET cc_start: 0.8170 (tpp) cc_final: 0.7856 (tpp)
REVERT: F   92 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8336 (ttp80)
REVERT: H   47 GLN cc_start: 0.8730 (tt0) cc_final: 0.8484 (tm-30)
REVERT: H   93 GLU cc_start: 0.8961 (mp0) cc_final: 0.8713 (mp0)
REVERT: H  116 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8849 (mmtp)
REVERT: L   32 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.8135 (m-70)
REVERT: L   63 LYS cc_start: 0.7436 (tptt) cc_final: 0.7092 (tppt)
REVERT: C   73 ASN cc_start: 0.9337 (t0) cc_final: 0.9043 (t0)
REVERT: C   90 ASP cc_start: 0.8542 (t70) cc_final: 0.8198 (t0)
REVERT: G   57 TYR cc_start: 0.8666 (t80) cc_final: 0.8435 (t80)
REVERT: G   90 ASP cc_start: 0.8574 (t70) cc_final: 0.8373 (t0)
  outliers start: 41
  outliers final: 27
  residues processed: 311
  average time/residue: 0.2915
  time to fit residues: 124.3091
Evaluate side-chains
  307 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 278
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   67 ARG
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   72 VAL
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  108 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 83 optimal weight:    0.0980
   chunk 0 optimal weight:   20.0000
   chunk 52 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 106 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 50 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 119 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
E  68 GLN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.083650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.059746 restraints weight = 74988.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.061521 restraints weight = 36027.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.062684 restraints weight = 23554.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14865  Z= 0.162
  Angle     :  0.702  13.705  21349  Z= 0.382
  Chirality :  0.038   0.248   2418
  Planarity :  0.004   0.047   1690
  Dihedral  : 29.712 155.757   4321
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 28.09 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.27), residues: 987
  helix:  1.27 (0.20), residues: 631
  sheet:  0.76 (1.09), residues: 24
  loop : -1.08 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP K  61 
 HIS   0.009   0.001   HIS L  75 
 PHE   0.014   0.001   PHE H  70 
 TYR   0.025   0.002   TYR B  88 
 ARG   0.012   0.001   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00017 (    2)
  link_TRANS           : angle       0.05059 (    6)
  hydrogen bonds       : bond        0.04057 (  844)
  hydrogen bonds       : angle       3.63664 ( 2154)
  metal coordination   : bond        0.00606 (    8)
  metal coordination   : angle       6.56137 (    9)
  covalent geometry    : bond        0.00360 (14855)
  covalent geometry    : angle       0.68950 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 292
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.7708 (m-80) cc_final: 0.7432 (m-10)
REVERT: A   64 LYS cc_start: 0.9106 (tppp) cc_final: 0.8869 (tppp)
REVERT: A   76 GLN cc_start: 0.8884 (pp30) cc_final: 0.8639 (pp30)
REVERT: A  125 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8804 (mm110)
REVERT: B   53 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: B   54 THR cc_start: 0.9404 (m) cc_final: 0.9187 (p)
REVERT: B   59 LYS cc_start: 0.9064 (tppt) cc_final: 0.8183 (tptp)
REVERT: B   88 TYR cc_start: 0.8427 (m-80) cc_final: 0.8057 (m-80)
REVERT: D   83 TYR cc_start: 0.7681 (m-10) cc_final: 0.7180 (m-10)
REVERT: D  105 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7911 (tm-30)
REVERT: D  109 HIS cc_start: 0.7999 (m-70) cc_final: 0.6787 (m170)
REVERT: E   73 GLU cc_start: 0.8704 (tt0) cc_final: 0.8442 (tt0)
REVERT: E   90 MET cc_start: 0.8007 (mmt) cc_final: 0.7680 (mmp)
REVERT: E  120 MET cc_start: 0.8947 (mmm) cc_final: 0.8368 (mmm)
REVERT: F   35 ARG cc_start: 0.9421 (ttp80) cc_final: 0.9076 (ttm110)
REVERT: F   63 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8585 (pm20)
REVERT: F   84 MET cc_start: 0.8181 (tpp) cc_final: 0.7773 (tpp)
REVERT: F   92 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8319 (ttp80)
REVERT: H   47 GLN cc_start: 0.8737 (tt0) cc_final: 0.8470 (tm-30)
REVERT: H   93 GLU cc_start: 0.8976 (mp0) cc_final: 0.8706 (mp0)
REVERT: H  116 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8604 (mmtp)
REVERT: K   20 MET cc_start: 0.8318 (mmp) cc_final: 0.8051 (tmm)
REVERT: K   63 ARG cc_start: 0.8435 (ptm-80) cc_final: 0.8233 (ptm-80)
REVERT: L   32 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.8100 (m-70)
REVERT: C   90 ASP cc_start: 0.8333 (t70) cc_final: 0.7914 (t0)
REVERT: G   57 TYR cc_start: 0.8667 (t80) cc_final: 0.8452 (t80)
REVERT: G   90 ASP cc_start: 0.8495 (t70) cc_final: 0.8043 (t0)
  outliers start: 34
  outliers final: 26
  residues processed: 305
  average time/residue: 0.2932
  time to fit residues: 123.7678
Evaluate side-chains
  307 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 279
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   72 VAL
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  108 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0770
   chunk 61 optimal weight:    7.9990
   chunk 83 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 92 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.6742

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E 108 ASN
F  64 ASN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.082078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.058119 restraints weight = 87094.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.059946 restraints weight = 39290.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.061145 restraints weight = 24918.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14865  Z= 0.192
  Angle     :  0.728  13.649  21349  Z= 0.396
  Chirality :  0.038   0.193   2418
  Planarity :  0.005   0.053   1690
  Dihedral  : 29.796 155.359   4321
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 28.32 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.27), residues: 987
  helix:  1.30 (0.20), residues: 630
  sheet:  0.55 (0.95), residues: 29
  loop : -1.20 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP K  61 
 HIS   0.008   0.001   HIS E  39 
 PHE   0.012   0.001   PHE H  70 
 TYR   0.023   0.002   TYR B  88 
 ARG   0.013   0.001   ARG K  67 

Details of bonding type rmsd
  link_TRANS           : bond        0.00067 (    2)
  link_TRANS           : angle       0.13434 (    6)
  hydrogen bonds       : bond        0.04391 (  844)
  hydrogen bonds       : angle       3.71865 ( 2154)
  metal coordination   : bond        0.01167 (    8)
  metal coordination   : angle       6.50851 (    9)
  covalent geometry    : bond        0.00432 (14855)
  covalent geometry    : angle       0.71572 (21334)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 286
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.8846 (tmm-80) cc_final: 0.8353 (tmm-80)
REVERT: A   54 TYR cc_start: 0.7599 (m-80) cc_final: 0.7378 (m-80)
REVERT: A   64 LYS cc_start: 0.9141 (tppp) cc_final: 0.8904 (tppp)
REVERT: A   76 GLN cc_start: 0.8927 (pp30) cc_final: 0.8702 (pp30)
REVERT: B   53 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8251 (mt-10)
REVERT: B   59 LYS cc_start: 0.9109 (tppt) cc_final: 0.8321 (tptp)
REVERT: D  109 HIS cc_start: 0.8117 (m-70) cc_final: 0.7249 (m170)
REVERT: E   90 MET cc_start: 0.8089 (mmt) cc_final: 0.7775 (mmp)
REVERT: E  120 MET cc_start: 0.8963 (mmm) cc_final: 0.8419 (mmm)
REVERT: F   84 MET cc_start: 0.8238 (tpp) cc_final: 0.5861 (tpp)
REVERT: F   92 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8326 (ttp80)
REVERT: H   47 GLN cc_start: 0.8754 (tt0) cc_final: 0.8456 (tm-30)
REVERT: H  116 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8631 (mmtp)
REVERT: K   63 ARG cc_start: 0.8596 (ptm-80) cc_final: 0.7850 (ptm-80)
REVERT: L   32 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.8116 (m-70)
REVERT: L   63 LYS cc_start: 0.7599 (tptt) cc_final: 0.7367 (tppt)
REVERT: C   90 ASP cc_start: 0.8315 (t70) cc_final: 0.7893 (t0)
REVERT: G   57 TYR cc_start: 0.8712 (t80) cc_final: 0.8493 (t80)
REVERT: G   90 ASP cc_start: 0.8460 (t70) cc_final: 0.7211 (t0)
  outliers start: 31
  outliers final: 26
  residues processed: 298
  average time/residue: 0.2929
  time to fit residues: 120.8339
Evaluate side-chains
  300 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 273
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   72 VAL
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  108 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 83 optimal weight:    0.1980
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 75 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
A 125 GLN
E  68 GLN
E 108 ASN
F  64 ASN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN
G  38 ASN
G  68 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.081326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.057812 restraints weight = 70578.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.059404 restraints weight = 34961.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.060523 restraints weight = 23301.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  14865  Z= 0.207
  Angle     :  0.740  13.717  21349  Z= 0.401
  Chirality :  0.039   0.210   2418
  Planarity :  0.005   0.047   1690
  Dihedral  : 29.901 153.859   4321
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 28.55 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 987
  helix:  1.26 (0.20), residues: 630
  sheet:  0.46 (0.95), residues: 29
  loop : -1.22 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP K  61 
 HIS   0.010   0.002   HIS K  65 
 PHE   0.012   0.001   PHE H  70 
 TYR   0.022   0.002   TYR B  88 
 ARG   0.012   0.001   ARG K  67 

Details of bonding type rmsd
  link_TRANS           : bond        0.00094 (    2)
  link_TRANS           : angle       0.19046 (    6)
  hydrogen bonds       : bond        0.04606 (  844)
  hydrogen bonds       : angle       3.80254 ( 2154)
  metal coordination   : bond        0.01360 (    8)
  metal coordination   : angle       6.49927 (    9)
  covalent geometry    : bond        0.00467 (14855)
  covalent geometry    : angle       0.72768 (21334)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5308.84 seconds
wall clock time: 92 minutes 59.51 seconds (5579.51 seconds total)