Starting phenix.real_space_refine
on Fri May 16 09:32:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn5_40613/05_2025/8sn5_40613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn5_40613/05_2025/8sn5_40613.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/8sn5_40613/05_2025/8sn5_40613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn5_40613/05_2025/8sn5_40613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn5_40613/05_2025/8sn5_40613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn5_40613/05_2025/8sn5_40613.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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14600
  Number of models: 1
  Model: ""
    Number of chains: 14
    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: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    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: "G"
      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: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    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: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    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  12296  SG  CYS K  31      32.772  74.839  47.610  1.00 92.05           S
  ATOM  12446  SG  CYS K  51      33.544  71.534  45.841  1.00 78.30           S
  ATOM  12470  SG  CYS K  54      32.537  74.397  43.794  1.00100.28           S
  ATOM  12187  SG  CYS K  16      22.380  68.849  53.466  1.00109.61           S
  ATOM  12205  SG  CYS K  19      20.326  66.237  55.227  1.00105.23           S
  ATOM  12335  SG  CYS K  36      23.285  67.916  57.089  1.00 94.72           S
  ATOM  12357  SG  CYS K  39      24.037  65.484  54.484  1.00 92.21           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 9.19, per 1000 atoms: 0.63
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (108.896, 134.128, 127.488, 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      33     16.00
     P     294     15.00
     O    3289      8.00
     N    2713      7.00
     C    8269      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: 3.71
  Conformation dependent library (CDL) restraints added in 1.3 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  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
      Number of angles added : 9


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 13 sheets defined
      63.6% alpha, 5.3% beta
      135 base pairs and 233 stacking pairs defined.
    Time for finding SS restraints: 7.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.502A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.794A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.921A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 4.203A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.476A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.813A  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 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.725A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.708A  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 46 through 55
    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 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.803A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.571A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    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
      removed outlier: 3.543A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.571A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.619A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.596A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 90
      removed outlier: 3.702A  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
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.773A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 4.256A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 39
      No H-bonds generated for 'chain 'M' and resid 37 through 39'
    Processing helix  chain 'M' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.679A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.738A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.809A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.826A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.004A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.679A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28
      removed outlier: 4.096A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16
      removed outlier: 3.623A  pdb=" N   VAL M   5 " --> pdb=" O   ILE M  13 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LEU M  15 " --> pdb=" O   ILE M   3 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE M   3 " --> pdb=" O   LEU M  15 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   LEU M  67 " --> pdb=" O   GLN M   2 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   PHE M   4 " --> pdb=" O   LEU M  67 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU M  69 " --> pdb=" O   PHE M   4 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LYS M   6 " --> pdb=" O   LEU M  69 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU M  71 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG M  42 " --> pdb=" O   VAL M  70 " (cutoff:3.500A)

    501 hydrogen bonds defined for protein.
    1464 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      233 stacking parallelities
  Total time for adding SS restraints: 5.98

  Time building geometry restraints manager: 4.34 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: 3384
        1.34 -     1.45: 4369
        1.45 -     1.57: 7084
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CA  ILE B  29 "
       pdb=" CB  ILE B  29 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.015 1.36e-02 5.41e+03 1.26e+00
  bond pdb=" CB  LYS M  48 "
       pdb=" CG  LYS M  48 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.17e+00
  bond pdb=" C   VAL K  24 "
       pdb=" N   GLU K  25 "
    ideal  model  delta    sigma   weight residual
    1.331  1.353 -0.022 2.07e-02 2.33e+03 1.15e+00
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.29e-01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 21557
        1.54 -     3.07: 551
        3.07 -     4.61: 41
        4.61 -     6.14: 16
        6.14 -     7.68: 6
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" N   TRP L 141 "
        pdb=" CA  TRP L 141 "
        pdb=" CB  TRP L 141 "
      ideal   model   delta    sigma   weight residual
     110.12  115.65   -5.53 1.47e+00 4.63e-01 1.41e+01
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  127.89   -6.35 1.91e+00 2.74e-01 1.10e+01
  angle pdb=" CB  LYS M  48 "
        pdb=" CG  LYS M  48 "
        pdb=" CD  LYS M  48 "
      ideal   model   delta    sigma   weight residual
     111.30  118.73   -7.43 2.30e+00 1.89e-01 1.04e+01
  angle pdb=" C   GLU L 140 "
        pdb=" N   TRP L 141 "
        pdb=" CA  TRP L 141 "
      ideal   model   delta    sigma   weight residual
     120.28  115.98    4.30 1.34e+00 5.57e-01 1.03e+01
  angle pdb=" CA  TRP L 141 "
        pdb=" CB  TRP L 141 "
        pdb=" CG  TRP L 141 "
      ideal   model   delta    sigma   weight residual
     113.60  118.60   -5.00 1.90e+00 2.77e-01 6.93e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 7298
       35.68 -    71.35: 1294
       71.35 -   107.03: 17
      107.03 -   142.70: 0
      142.70 -   178.38: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.38 -178.38     1      3.50e+01 8.16e-04 1.57e+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   76.32  143.68     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CA  ARG L 131 "
           pdb=" C   ARG L 131 "
           pdb=" N   ASP L 132 "
           pdb=" CA  ASP L 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.15  -17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1794
       0.031 -    0.061: 526
       0.061 -    0.092: 118
       0.092 -    0.123: 66
       0.123 -    0.153: 12
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CA  GLN A 125 "
            pdb=" N   GLN A 125 "
            pdb=" C   GLN A 125 "
            pdb=" CB  GLN A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.78e-01
  chirality pdb=" CA  GLU K  25 "
            pdb=" N   GLU K  25 "
            pdb=" C   GLU K  25 "
            pdb=" CB  GLU K  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.52e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L 141 "    0.030 2.00e-02 2.50e+03   2.98e-02 2.23e+01
        pdb=" CG  TRP L 141 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD1 TRP L 141 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP L 141 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP L 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP L 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP L 141 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP L 141 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.022 2.00e-02 2.50e+03   9.23e-03 2.34e+00
        pdb=" N9   DA I -35 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -54 "    0.020 2.00e-02 2.50e+03   9.03e-03 2.24e+00
        pdb=" N9   DA I -54 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8   DA I -54 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I -54 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I -54 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -54 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -54 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -54 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I -54 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3   DA I -54 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -54 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 413
        2.68 -     3.24: 13032
        3.24 -     3.79: 26278
        3.79 -     4.35: 32109
        4.35 -     4.90: 47543
  Nonbonded interactions: 119375
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.131 2.496
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER L  91 "
            pdb=" OE1 GLN L  92 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD1 ASP L 130 "
            pdb=" NZ  LYS L 133 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" OE2 GLU A  94 "
            pdb=" NE2 GLN G 104 "
     model   vdw
     2.243 3.120
  ... (remaining 119370 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 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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=0.17 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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     43.220
  Find NCS groups from input model:        0.370
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
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   0.059  15482  Z= 0.152
  Angle     :  0.574   7.753  22186  Z= 0.329
  Chirality :  0.035   0.153   2516
  Planarity :  0.004   0.037   1794
  Dihedral  : 25.638 178.379   6577
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.27), residues: 1057
  helix:  2.63 (0.21), residues: 646
  sheet:  0.85 (0.75), residues: 47
  loop : -0.56 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.005   TRP L 141 
 HIS   0.005   0.001   HIS D 109 
 PHE   0.006   0.001   PHE D  70 
 TYR   0.018   0.001   TYR H  40 
 ARG   0.006   0.000   ARG L 131 

Details of bonding type rmsd
  link_TRANS           : bond        0.00088 (    2)
  link_TRANS           : angle       0.68680 (    6)
  hydrogen bonds       : bond        0.10388 (  848)
  hydrogen bonds       : angle       3.98729 ( 2154)
  metal coordination   : bond        0.02151 (    8)
  metal coordination   : angle       3.91026 (    9)
  covalent geometry    : bond        0.00328 (15472)
  covalent geometry    : angle       0.56875 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9152 (mt) cc_final: 0.8940 (mt)
REVERT: C   39 TYR cc_start: 0.8837 (m-80) cc_final: 0.8516 (m-80)
REVERT: D  108 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8001 (mtmt)
REVERT: H   35 GLU cc_start: 0.8641 (mp0) cc_final: 0.8421 (mp0)
REVERT: H   89 ILE cc_start: 0.9224 (mt) cc_final: 0.9005 (mt)
REVERT: K   13 GLU cc_start: 0.8434 (tp30) cc_final: 0.8139 (tm-30)
REVERT: L   60 TYR cc_start: 0.7143 (t80) cc_final: 0.6810 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.3392
  time to fit residues: 130.9766
Evaluate side-chains
  226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0070
   chunk 101 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 117 optimal weight:    7.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  38 ASN
K  81 GLN
K  83 HIS
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  46 GLN
M   2 GLN
M  25 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.121298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.080647 restraints weight = 38775.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.083034 restraints weight = 26835.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.082409 restraints weight = 19660.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15482  Z= 0.162
  Angle     :  0.602  11.511  22186  Z= 0.337
  Chirality :  0.036   0.161   2516
  Planarity :  0.004   0.043   1794
  Dihedral  : 28.845 178.604   4413
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.20 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.27), residues: 1057
  helix:  2.61 (0.21), residues: 653
  sheet:  0.57 (0.70), residues: 50
  loop : -0.61 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.004   TRP L 141 
 HIS   0.006   0.001   HIS L  75 
 PHE   0.014   0.001   PHE L  62 
 TYR   0.015   0.002   TYR L  74 
 ARG   0.007   0.000   ARG D  86 

Details of bonding type rmsd
  link_TRANS           : bond        0.00085 (    2)
  link_TRANS           : angle       0.37143 (    6)
  hydrogen bonds       : bond        0.04379 (  848)
  hydrogen bonds       : angle       3.39731 ( 2154)
  metal coordination   : bond        0.01553 (    8)
  metal coordination   : angle       6.13744 (    9)
  covalent geometry    : bond        0.00359 (15472)
  covalent geometry    : angle       0.58897 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 246
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9175 (t) cc_final: 0.7929 (t)
REVERT: A   59 GLU cc_start: 0.8912 (pm20) cc_final: 0.8458 (pm20)
REVERT: A  120 MET cc_start: 0.8142 (mtt) cc_final: 0.7853 (mtt)
REVERT: A  125 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7339 (pm20)
REVERT: D   88 THR cc_start: 0.9393 (m) cc_final: 0.8958 (p)
REVERT: D  108 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8093 (mtmt)
REVERT: F   88 TYR cc_start: 0.8731 (m-80) cc_final: 0.8493 (m-80)
REVERT: H   35 GLU cc_start: 0.8936 (mp0) cc_final: 0.8649 (mp0)
REVERT: L   60 TYR cc_start: 0.7372 (t80) cc_final: 0.6973 (t80)
REVERT: L   88 ILE cc_start: 0.8593 (mp) cc_final: 0.8381 (mp)
  outliers start: 11
  outliers final: 8
  residues processed: 251
  average time/residue: 0.2979
  time to fit residues: 104.3136
Evaluate side-chains
  231 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 222
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 128 optimal weight:    0.1980
   chunk 50 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0060
   chunk 42 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  38 ASN
H  47 GLN
K  32 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  55 HIS
M  25 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.122546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.087108 restraints weight = 63965.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.090385 restraints weight = 47888.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.090012 restraints weight = 26278.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15482  Z= 0.144
  Angle     :  0.575  12.059  22186  Z= 0.324
  Chirality :  0.034   0.146   2516
  Planarity :  0.004   0.045   1794
  Dihedral  : 28.896 178.727   4413
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.61 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.26), residues: 1057
  helix:  2.56 (0.21), residues: 654
  sheet:  0.80 (0.68), residues: 49
  loop : -0.65 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L 141 
 HIS   0.003   0.001   HIS K  65 
 PHE   0.012   0.001   PHE L  62 
 TYR   0.014   0.001   TYR E  99 
 ARG   0.005   0.000   ARG G  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00023 (    2)
  link_TRANS           : angle       0.30796 (    6)
  hydrogen bonds       : bond        0.04027 (  848)
  hydrogen bonds       : angle       3.25650 ( 2154)
  metal coordination   : bond        0.01255 (    8)
  metal coordination   : angle       5.35235 (    9)
  covalent geometry    : bond        0.00311 (15472)
  covalent geometry    : angle       0.56495 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 238
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9112 (t) cc_final: 0.7762 (t)
REVERT: A   59 GLU cc_start: 0.8804 (pm20) cc_final: 0.8166 (pm20)
REVERT: A  120 MET cc_start: 0.8192 (mtt) cc_final: 0.7941 (mtt)
REVERT: A  123 ASP cc_start: 0.8840 (m-30) cc_final: 0.8633 (m-30)
REVERT: A  125 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7134 (pm20)
REVERT: B   63 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8075 (mt-10)
REVERT: D   88 THR cc_start: 0.9182 (m) cc_final: 0.8806 (p)
REVERT: D  108 LYS cc_start: 0.8310 (ttpt) cc_final: 0.8028 (mtmt)
REVERT: F   88 TYR cc_start: 0.8611 (m-80) cc_final: 0.8283 (m-80)
REVERT: G  118 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7814 (tmtt)
REVERT: H   35 GLU cc_start: 0.8905 (mp0) cc_final: 0.8576 (mp0)
REVERT: K   20 MET cc_start: 0.7608 (mmp) cc_final: 0.7385 (mmp)
REVERT: L   60 TYR cc_start: 0.7410 (t80) cc_final: 0.7083 (t80)
REVERT: L   88 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8196 (mp)
  outliers start: 12
  outliers final: 6
  residues processed: 242
  average time/residue: 0.3056
  time to fit residues: 102.8523
Evaluate side-chains
  223 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 215
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 72 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 60 optimal weight:    0.2980
   chunk 98 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
K  32 ASN
K  41 GLN
L  46 GLN
L  55 HIS
M  25 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.120465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.085730 restraints weight = 56563.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.087725 restraints weight = 56341.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.088022 restraints weight = 32997.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15482  Z= 0.168
  Angle     :  0.590  11.690  22186  Z= 0.330
  Chirality :  0.035   0.171   2516
  Planarity :  0.004   0.045   1794
  Dihedral  : 29.024 178.520   4413
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.56 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.27), residues: 1057
  helix:  2.57 (0.21), residues: 654
  sheet:  0.81 (0.67), residues: 48
  loop : -0.72 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L 141 
 HIS   0.004   0.001   HIS D 109 
 PHE   0.012   0.001   PHE L  62 
 TYR   0.037   0.002   TYR L 134 
 ARG   0.007   0.000   ARG G  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00093 (    2)
  link_TRANS           : angle       0.36467 (    6)
  hydrogen bonds       : bond        0.04411 (  848)
  hydrogen bonds       : angle       3.32721 ( 2154)
  metal coordination   : bond        0.01643 (    8)
  metal coordination   : angle       5.82065 (    9)
  covalent geometry    : bond        0.00378 (15472)
  covalent geometry    : angle       0.57806 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 232
  time to evaluate  : 1.129 
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   57 SER cc_start: 0.9071 (t) cc_final: 0.7758 (t)
REVERT: A   59 GLU cc_start: 0.8911 (pm20) cc_final: 0.8224 (pm20)
REVERT: A  123 ASP cc_start: 0.8869 (m-30) cc_final: 0.8570 (m-30)
REVERT: A  125 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7263 (pm20)
REVERT: B   63 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8087 (mt-10)
REVERT: D  108 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8062 (mtmt)
REVERT: F   88 TYR cc_start: 0.8909 (m-80) cc_final: 0.8485 (m-10)
REVERT: H   35 GLU cc_start: 0.8791 (mp0) cc_final: 0.8513 (mp0)
REVERT: H   51 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8088 (t0)
REVERT: K   68 ARG cc_start: 0.6856 (mtm110) cc_final: 0.6455 (mtm110)
REVERT: L   31 PHE cc_start: 0.7806 (m-10) cc_final: 0.7464 (m-80)
REVERT: L   88 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8169 (mp)
  outliers start: 20
  outliers final: 13
  residues processed: 236
  average time/residue: 0.2857
  time to fit residues: 94.2944
Evaluate side-chains
  232 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 216
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 125 optimal weight:    0.0040
   chunk 47 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 2 optimal weight:    0.4980
   chunk 112 optimal weight:   20.0000
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.122621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.087825 restraints weight = 52413.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.087417 restraints weight = 50462.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.088515 restraints weight = 39236.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.144
  Angle     :  0.584  11.979  22186  Z= 0.326
  Chirality :  0.035   0.172   2516
  Planarity :  0.004   0.042   1794
  Dihedral  : 28.945 178.818   4413
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.07 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.26), residues: 1057
  helix:  2.57 (0.21), residues: 654
  sheet:  0.70 (0.68), residues: 48
  loop : -0.70 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP L 141 
 HIS   0.010   0.001   HIS K  65 
 PHE   0.014   0.001   PHE L  62 
 TYR   0.016   0.001   TYR E  99 
 ARG   0.006   0.000   ARG D  86 

Details of bonding type rmsd
  link_TRANS           : bond        0.00020 (    2)
  link_TRANS           : angle       0.32484 (    6)
  hydrogen bonds       : bond        0.03941 (  848)
  hydrogen bonds       : angle       3.14395 ( 2154)
  metal coordination   : bond        0.01428 (    8)
  metal coordination   : angle       5.30980 (    9)
  covalent geometry    : bond        0.00312 (15472)
  covalent geometry    : angle       0.57399 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 231
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9023 (t) cc_final: 0.7658 (t)
REVERT: A   59 GLU cc_start: 0.8894 (pm20) cc_final: 0.8220 (pm20)
REVERT: A  123 ASP cc_start: 0.8799 (m-30) cc_final: 0.8492 (m-30)
REVERT: A  125 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7169 (pm20)
REVERT: B   63 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: D  108 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8025 (mtmt)
REVERT: F   88 TYR cc_start: 0.8786 (m-80) cc_final: 0.8509 (m-10)
REVERT: H   35 GLU cc_start: 0.8795 (mp0) cc_final: 0.8506 (mp0)
REVERT: H  120 LYS cc_start: 0.9123 (ttmm) cc_final: 0.8919 (ttmm)
REVERT: K   41 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8589 (tp40)
REVERT: K   64 TYR cc_start: 0.8474 (t80) cc_final: 0.7731 (t80)
REVERT: L   88 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8228 (mp)
  outliers start: 19
  outliers final: 14
  residues processed: 240
  average time/residue: 0.2841
  time to fit residues: 96.5853
Evaluate side-chains
  237 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 220
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 118 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** L  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.119412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.082573 restraints weight = 54226.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.084109 restraints weight = 40281.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.083889 restraints weight = 33649.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  15482  Z= 0.183
  Angle     :  0.616  12.613  22186  Z= 0.340
  Chirality :  0.036   0.162   2516
  Planarity :  0.004   0.048   1794
  Dihedral  : 29.047 178.355   4413
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.40 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.27), residues: 1057
  helix:  2.46 (0.21), residues: 660
  sheet:  0.45 (0.69), residues: 48
  loop : -0.83 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP L 141 
 HIS   0.012   0.001   HIS K  65 
 PHE   0.018   0.001   PHE L  62 
 TYR   0.017   0.002   TYR E  99 
 ARG   0.005   0.000   ARG D  86 

Details of bonding type rmsd
  link_TRANS           : bond        0.00121 (    2)
  link_TRANS           : angle       0.37382 (    6)
  hydrogen bonds       : bond        0.04520 (  848)
  hydrogen bonds       : angle       3.32290 ( 2154)
  metal coordination   : bond        0.01806 (    8)
  metal coordination   : angle       5.80018 (    9)
  covalent geometry    : bond        0.00416 (15472)
  covalent geometry    : angle       0.60450 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 221
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9134 (t) cc_final: 0.8922 (t)
REVERT: A  123 ASP cc_start: 0.9012 (m-30) cc_final: 0.8742 (m-30)
REVERT: A  125 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7127 (pm20)
REVERT: B   63 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8082 (mt-10)
REVERT: C   13 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7665 (mptt)
REVERT: D  108 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8130 (mtmt)
REVERT: F   84 MET cc_start: 0.8912 (mmm) cc_final: 0.8633 (mmm)
REVERT: F   88 TYR cc_start: 0.9008 (m-10) cc_final: 0.8572 (m-10)
REVERT: H   35 GLU cc_start: 0.8869 (mp0) cc_final: 0.8532 (mp0)
REVERT: K   21 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7413 (mm-30)
REVERT: K   41 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8776 (tp40)
REVERT: K   68 ARG cc_start: 0.6882 (mtm110) cc_final: 0.6659 (mtm110)
REVERT: L    8 LYS cc_start: 0.9185 (mttp) cc_final: 0.8933 (mtmm)
REVERT: L   31 PHE cc_start: 0.8118 (m-80) cc_final: 0.7496 (t80)
REVERT: L   88 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8292 (mp)
  outliers start: 25
  outliers final: 19
  residues processed: 230
  average time/residue: 0.2888
  time to fit residues: 93.3721
Evaluate side-chains
  238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 128 optimal weight:    0.0770
   chunk 73 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0770
   chunk 92 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 118 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
K  41 GLN
L  46 GLN
** L  75 HIS ** 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 = 0.3701 r_free = 0.3701 target = 0.121526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.085402 restraints weight = 57832.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.088262 restraints weight = 43576.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.087845 restraints weight = 29244.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15482  Z= 0.146
  Angle     :  0.593  12.779  22186  Z= 0.329
  Chirality :  0.035   0.163   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 28.969 178.726   4413
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.16 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.27), residues: 1057
  helix:  2.52 (0.21), residues: 660
  sheet:  0.33 (0.69), residues: 48
  loop : -0.82 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.004   TRP L 141 
 HIS   0.008   0.001   HIS K  65 
 PHE   0.011   0.001   PHE L  62 
 TYR   0.027   0.002   TYR L 134 
 ARG   0.006   0.000   ARG D  86 

Details of bonding type rmsd
  link_TRANS           : bond        0.00036 (    2)
  link_TRANS           : angle       0.26716 (    6)
  hydrogen bonds       : bond        0.04087 (  848)
  hydrogen bonds       : angle       3.17201 ( 2154)
  metal coordination   : bond        0.01609 (    8)
  metal coordination   : angle       5.40480 (    9)
  covalent geometry    : bond        0.00319 (15472)
  covalent geometry    : angle       0.58303 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 230
  time to evaluate  : 1.135 
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  123 ASP cc_start: 0.8930 (m-30) cc_final: 0.8662 (m-30)
REVERT: A  125 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7152 (pm20)
REVERT: B   63 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8047 (mt-10)
REVERT: C   13 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7709 (mptt)
REVERT: D  108 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8103 (mtmt)
REVERT: E   39 HIS cc_start: 0.8327 (t-90) cc_final: 0.8061 (t-90)
REVERT: F   84 MET cc_start: 0.8872 (mmm) cc_final: 0.8606 (mmm)
REVERT: F   88 TYR cc_start: 0.8969 (m-10) cc_final: 0.8640 (m-10)
REVERT: H   35 GLU cc_start: 0.8876 (mp0) cc_final: 0.8538 (mp0)
REVERT: H   51 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (t0)
REVERT: H  120 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8954 (ttmm)
REVERT: K   68 ARG cc_start: 0.6951 (mtm110) cc_final: 0.6240 (mtm110)
REVERT: K   84 TYR cc_start: 0.7670 (m-80) cc_final: 0.6702 (m-80)
REVERT: L   31 PHE cc_start: 0.8065 (m-80) cc_final: 0.7822 (m-80)
REVERT: L   88 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: M    1 MET cc_start: 0.5336 (tmm) cc_final: 0.4749 (tpt)
  outliers start: 21
  outliers final: 16
  residues processed: 238
  average time/residue: 0.2811
  time to fit residues: 95.3337
Evaluate side-chains
  238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 219
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 123 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 126 optimal weight:    8.9990
   chunk 109 optimal weight:    0.6980
   chunk 115 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0050
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
K  32 ASN
K  41 GLN
** L  75 HIS ** 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 = 0.3710 r_free = 0.3710 target = 0.122096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.085709 restraints weight = 56044.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.087980 restraints weight = 40135.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.087544 restraints weight = 31465.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15482  Z= 0.146
  Angle     :  0.601  13.597  22186  Z= 0.332
  Chirality :  0.035   0.163   2516
  Planarity :  0.004   0.051   1794
  Dihedral  : 28.946 178.437   4413
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.56 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.27), residues: 1057
  helix:  2.57 (0.21), residues: 660
  sheet:  0.05 (0.67), residues: 42
  loop : -0.85 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.087   0.005   TRP L 141 
 HIS   0.009   0.001   HIS K  65 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.027   0.002   TYR L 145 
 ARG   0.007   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00030 (    2)
  link_TRANS           : angle       0.23252 (    6)
  hydrogen bonds       : bond        0.04028 (  848)
  hydrogen bonds       : angle       3.24387 ( 2154)
  metal coordination   : bond        0.01489 (    8)
  metal coordination   : angle       5.17991 (    9)
  covalent geometry    : bond        0.00319 (15472)
  covalent geometry    : angle       0.59251 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 222
  time to evaluate  : 1.126 
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   59 GLU cc_start: 0.8799 (pm20) cc_final: 0.8453 (pm20)
REVERT: A  123 ASP cc_start: 0.8932 (m-30) cc_final: 0.8672 (m-30)
REVERT: A  125 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7252 (pm20)
REVERT: B   63 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: D  108 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8077 (mtmt)
REVERT: E   39 HIS cc_start: 0.8289 (t-90) cc_final: 0.8040 (t-90)
REVERT: E   94 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8172 (mm-30)
REVERT: F   84 MET cc_start: 0.8861 (mmm) cc_final: 0.8653 (mmm)
REVERT: F   88 TYR cc_start: 0.8963 (m-10) cc_final: 0.8651 (m-10)
REVERT: H   35 GLU cc_start: 0.8882 (mp0) cc_final: 0.8542 (mp0)
REVERT: K   41 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8843 (tp40)
REVERT: K   68 ARG cc_start: 0.6954 (mtm110) cc_final: 0.6243 (mtm110)
REVERT: K   84 TYR cc_start: 0.7679 (m-80) cc_final: 0.6669 (m-80)
REVERT: L   31 PHE cc_start: 0.8067 (m-80) cc_final: 0.7832 (m-80)
REVERT: L   88 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (mp)
REVERT: M    1 MET cc_start: 0.5161 (tmm) cc_final: 0.4640 (tpt)
REVERT: M   52 ASP cc_start: 0.6845 (m-30) cc_final: 0.6044 (m-30)
  outliers start: 21
  outliers final: 16
  residues processed: 232
  average time/residue: 0.2914
  time to fit residues: 96.2223
Evaluate side-chains
  234 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 215
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 117 optimal weight:    0.2980
   chunk 73 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0370
   chunk 23 optimal weight:    0.3980
   chunk 72 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   chunk 84 optimal weight:    5.9990
   overall best weight:    0.3458

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
K  41 GLN
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.127303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.091593 restraints weight = 46177.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.093047 restraints weight = 29577.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.093135 restraints weight = 28696.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15482  Z= 0.143
  Angle     :  0.615  13.085  22186  Z= 0.337
  Chirality :  0.035   0.170   2516
  Planarity :  0.004   0.046   1794
  Dihedral  : 28.918 178.207   4413
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.21 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.27), residues: 1057
  helix:  2.56 (0.21), residues: 659
  sheet:  0.06 (0.68), residues: 42
  loop : -0.85 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.089   0.005   TRP L 141 
 HIS   0.008   0.001   HIS K  65 
 PHE   0.011   0.001   PHE L  62 
 TYR   0.035   0.002   TYR L 145 
 ARG   0.007   0.000   ARG D  86 

Details of bonding type rmsd
  link_TRANS           : bond        0.00009 (    2)
  link_TRANS           : angle       0.21469 (    6)
  hydrogen bonds       : bond        0.03988 (  848)
  hydrogen bonds       : angle       3.16480 ( 2154)
  metal coordination   : bond        0.01336 (    8)
  metal coordination   : angle       5.68711 (    9)
  covalent geometry    : bond        0.00311 (15472)
  covalent geometry    : angle       0.60493 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 227
  time to evaluate  : 1.163 
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   59 GLU cc_start: 0.8727 (pm20) cc_final: 0.8243 (pm20)
REVERT: A  123 ASP cc_start: 0.8803 (m-30) cc_final: 0.8527 (m-30)
REVERT: A  125 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7243 (pm20)
REVERT: B   67 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7963 (ttp-170)
REVERT: D  108 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8012 (mtmt)
REVERT: D  116 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8667 (ttpt)
REVERT: E   39 HIS cc_start: 0.8302 (t-90) cc_final: 0.8074 (t-90)
REVERT: E   61 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9043 (mm)
REVERT: E   94 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8115 (mm-30)
REVERT: F   84 MET cc_start: 0.8846 (mmm) cc_final: 0.8627 (mmm)
REVERT: H   35 GLU cc_start: 0.8861 (mp0) cc_final: 0.8501 (mp0)
REVERT: K   41 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8868 (tp40)
REVERT: K   67 ARG cc_start: 0.7800 (tpp80) cc_final: 0.6396 (ttp-110)
REVERT: K   68 ARG cc_start: 0.6954 (mtm110) cc_final: 0.6214 (mtm110)
REVERT: K   84 TYR cc_start: 0.7626 (m-80) cc_final: 0.6653 (m-80)
REVERT: L   31 PHE cc_start: 0.7971 (m-80) cc_final: 0.7755 (m-80)
REVERT: L   88 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: M    1 MET cc_start: 0.5015 (tmm) cc_final: 0.4514 (tpt)
  outliers start: 19
  outliers final: 14
  residues processed: 236
  average time/residue: 0.2951
  time to fit residues: 97.7674
Evaluate side-chains
  240 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 222
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 45 optimal weight:    0.4980
   chunk 101 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0370
   chunk 62 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
K  32 ASN
K  41 GLN
** L  75 HIS ** 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 = 0.3804 r_free = 0.3804 target = 0.127661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.092735 restraints weight = 45070.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.093442 restraints weight = 32361.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.093907 restraints weight = 34898.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15482  Z= 0.146
  Angle     :  0.629  14.221  22186  Z= 0.344
  Chirality :  0.035   0.220   2516
  Planarity :  0.004   0.047   1794
  Dihedral  : 28.929 177.946   4413
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.21 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.27), residues: 1057
  helix:  2.54 (0.21), residues: 659
  sheet:  0.02 (0.69), residues: 42
  loop : -0.87 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.109   0.006   TRP L 141 
 HIS   0.008   0.001   HIS K  65 
 PHE   0.017   0.001   PHE K  40 
 TYR   0.024   0.002   TYR F  88 
 ARG   0.007   0.000   ARG D  86 

Details of bonding type rmsd
  link_TRANS           : bond        0.00019 (    2)
  link_TRANS           : angle       0.20254 (    6)
  hydrogen bonds       : bond        0.04031 (  848)
  hydrogen bonds       : angle       3.18615 ( 2154)
  metal coordination   : bond        0.01405 (    8)
  metal coordination   : angle       5.08068 (    9)
  covalent geometry    : bond        0.00319 (15472)
  covalent geometry    : angle       0.62128 (22171)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 229
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8718 (pm20) cc_final: 0.8222 (pm20)
REVERT: A  123 ASP cc_start: 0.8790 (m-30) cc_final: 0.8515 (m-30)
REVERT: A  125 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7277 (pm20)
REVERT: B   67 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7930 (ttp-170)
REVERT: D   59 MET cc_start: 0.8296 (tpp) cc_final: 0.7697 (tpp)
REVERT: D  108 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8030 (mtmt)
REVERT: E   39 HIS cc_start: 0.8315 (t-90) cc_final: 0.8102 (t-90)
REVERT: E   61 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9047 (mm)
REVERT: E   94 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8112 (mm-30)
REVERT: H   35 GLU cc_start: 0.8836 (mp0) cc_final: 0.8499 (mp0)
REVERT: K   41 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8885 (tp40)
REVERT: K   67 ARG cc_start: 0.7784 (tpp80) cc_final: 0.6421 (ttp-110)
REVERT: K   68 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6408 (mtm110)
REVERT: K   84 TYR cc_start: 0.7592 (m-80) cc_final: 0.6560 (m-80)
REVERT: L    4 LYS cc_start: 0.8963 (ptmt) cc_final: 0.8591 (pttt)
REVERT: L   88 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8117 (mp)
REVERT: L  147 MET cc_start: 0.7164 (mmp) cc_final: 0.6461 (ptp)
REVERT: M    1 MET cc_start: 0.4928 (tmm) cc_final: 0.4385 (tpt)
REVERT: M   52 ASP cc_start: 0.6372 (m-30) cc_final: 0.6111 (m-30)
  outliers start: 20
  outliers final: 16
  residues processed: 238
  average time/residue: 0.2922
  time to fit residues: 97.6958
Evaluate side-chains
  242 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 222
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 111 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 115 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
K  41 GLN
** L  75 HIS ** 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 = 0.3668 r_free = 0.3668 target = 0.118332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.072564 restraints weight = 70426.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.075216 restraints weight = 37076.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.078111 restraints weight = 20215.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.091  15482  Z= 0.379
  Angle     :  0.817  13.423  22186  Z= 0.444
  Chirality :  0.045   0.220   2516
  Planarity :  0.006   0.051   1794
  Dihedral  : 29.371 176.900   4413
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.32 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.26), residues: 1057
  helix:  1.69 (0.20), residues: 658
  sheet: -0.13 (0.69), residues: 48
  loop : -1.09 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.096   0.006   TRP L 141 
 HIS   0.015   0.002   HIS K  65 
 PHE   0.021   0.002   PHE L  62 
 TYR   0.043   0.004   TYR D  83 
 ARG   0.008   0.001   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00397 (    2)
  link_TRANS           : angle       0.47421 (    6)
  hydrogen bonds       : bond        0.06763 (  848)
  hydrogen bonds       : angle       4.15204 ( 2154)
  metal coordination   : bond        0.03265 (    8)
  metal coordination   : angle       7.13016 (    9)
  covalent geometry    : bond        0.00889 (15472)
  covalent geometry    : angle       0.80458 (22171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4539.87 seconds
wall clock time: 79 minutes 50.61 seconds (4790.61 seconds total)