Starting phenix.real_space_refine
on Mon Jun 16 07:15:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smy_40606/06_2025/8smy_40606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smy_40606/06_2025/8smy_40606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smy_40606/06_2025/8smy_40606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smy_40606/06_2025/8smy_40606.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smy_40606/06_2025/8smy_40606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smy_40606/06_2025/8smy_40606.cif"
  }
  resolution = 3.2
  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=   0.115
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7891      2.51       5
     N    2608      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13998
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "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: "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      32.961  68.212  47.437  1.00 46.50           S
  ATOM  12446  SG  CYS K  51      31.741  64.804  46.427  1.00 38.48           S
  ATOM  12470  SG  CYS K  54      31.689  67.804  43.930  1.00 45.98           S
  ATOM  12187  SG  CYS K  16      23.164  61.088  52.931  1.00 62.13           S
  ATOM  12205  SG  CYS K  19      21.277  58.686  55.106  1.00 60.25           S
  ATOM  12335  SG  CYS K  36      24.123  60.787  56.601  1.00 49.24           S
  ATOM  12357  SG  CYS K  39      25.001  57.974  54.445  1.00 47.55           S

  Time building chain proxies: 9.42, per 1000 atoms: 0.67
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 130.144, 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      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2608      7.00
     C    7891      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: 3.53
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        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  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 11 sheets defined
      63.4% alpha, 4.3% beta
      137 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 6.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 55
      removed outlier: 3.697A  pdb=" N   ILE A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.706A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.642A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.836A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.608A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.724A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.737A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.541A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.564A  pdb=" N   MET D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 4.180A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.618A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU E 105 " --> pdb=" O   VAL E 101 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.881A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.595A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.757A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 90
    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
      removed outlier: 3.620A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 4.044A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.656A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.887A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.703A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
    Processing helix  chain 'L' and resid 131 through 145
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.687A  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: 3.535A  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 96 through 98
      removed outlier: 6.696A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.458A  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 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=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.097A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.767A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 29
      removed outlier: 3.788A  pdb=" N   HIS K  33 " --> pdb=" O   LEU K  29 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25

    452 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      351 hydrogen bonds
      698 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 5.13

  Time building geometry restraints manager: 4.26 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: 3240
        1.34 -     1.46: 4293
        1.46 -     1.58: 6698
        1.58 -     1.70: 586
        1.70 -     1.82: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.74e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.60e+00
  bond pdb=" CG  ARG A  42 "
       pdb=" CD  ARG A  42 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.29e+00
  bond pdb=" CA  ASN L  79 "
       pdb=" C   ASN L  79 "
    ideal  model  delta    sigma   weight residual
    1.528  1.540 -0.012 1.33e-02 5.65e+03 8.57e-01
  bond pdb=" CB  PRO L  61 "
       pdb=" CG  PRO L  61 "
    ideal  model  delta    sigma   weight residual
    1.506  1.471  0.035 3.90e-02 6.57e+02 8.17e-01
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 20972
        1.75 -     3.50: 360
        3.50 -     5.25: 17
        5.25 -     6.99: 2
        6.99 -     8.74: 2
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" C   TYR L  60 "
        pdb=" N   PRO L  61 "
        pdb=" CD  PRO L  61 "
      ideal   model   delta    sigma   weight residual
     120.60  111.86    8.74 2.20e+00 2.07e-01 1.58e+01
  angle pdb=" C   SER L  80 "
        pdb=" N   ASN L  81 "
        pdb=" CA  ASN L  81 "
      ideal   model   delta    sigma   weight residual
     121.94  116.43    5.51 2.00e+00 2.50e-01 7.60e+00
  angle pdb=" N   GLU L 140 "
        pdb=" CA  GLU L 140 "
        pdb=" CB  GLU L 140 "
      ideal   model   delta    sigma   weight residual
     110.28  113.97   -3.69 1.55e+00 4.16e-01 5.68e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  118.29   -5.11 2.37e+00 1.78e-01 4.64e+00
  angle pdb=" CA  LEU K  49 "
        pdb=" CB  LEU K  49 "
        pdb=" CG  LEU K  49 "
      ideal   model   delta    sigma   weight residual
     116.30  123.63   -7.33 3.50e+00 8.16e-02 4.39e+00
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.30: 6813
       35.30 -    70.59: 1393
       70.59 -   105.89: 22
      105.89 -   141.19: 0
      141.19 -   176.49: 2
  Dihedral angle restraints: 8230
    sinusoidal: 5306
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.51  176.49     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   66.28  153.72     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CB  GLU G  41 "
           pdb=" CG  GLU G  41 "
           pdb=" CD  GLU G  41 "
           pdb=" OE1 GLU G  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.70  -89.70     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1478
       0.025 -    0.051: 607
       0.051 -    0.076: 238
       0.076 -    0.101: 60
       0.101 -    0.126: 36
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CA  ILE G  79 "
            pdb=" N   ILE G  79 "
            pdb=" C   ILE G  79 "
            pdb=" CB  ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality pdb=" CA  ILE L  78 "
            pdb=" N   ILE L  78 "
            pdb=" C   ILE L  78 "
            pdb=" CB  ILE L  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  ILE D  89 "
            pdb=" N   ILE D  89 "
            pdb=" C   ILE D  89 "
            pdb=" CB  ILE D  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "   -0.053 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO L  61 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  42 "   -0.182 9.50e-02 1.11e+02   8.19e-02 4.21e+00
        pdb=" NE  ARG A  42 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  42 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  42 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  42 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS L  75 "   -0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO L  76 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO L  76 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO L  76 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 610
        2.71 -     3.26: 12002
        3.26 -     3.80: 24351
        3.80 -     4.35: 31976
        4.35 -     4.90: 46643
  Nonbonded interactions: 115582
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  73 "
            pdb=" ND2 ASN B  25 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" OG  SER K  60 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.244 2.496
  nonbonded pdb=" O   LEU E  61 "
            pdb=" NH1 ARG F  36 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.271 3.120
  ... (remaining 115577 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.130
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     43.270
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14874  Z= 0.142
  Angle     :  0.540   8.742  21368  Z= 0.319
  Chirality :  0.034   0.126   2419
  Planarity :  0.005   0.082   1688
  Dihedral  : 26.398 176.486   6336
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.27), residues: 983
  helix:  1.87 (0.22), residues: 613
  sheet:  0.67 (1.00), residues: 24
  loop : -0.77 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  77 
 HIS   0.005   0.001   HIS L  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.012   0.001   TYR L 134 
 ARG   0.009   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00192 (    2)
  link_TRANS           : angle       0.58269 (    6)
  hydrogen bonds       : bond        0.11106 (  803)
  hydrogen bonds       : angle       3.48440 ( 2033)
  metal coordination   : bond        0.01386 (    8)
  metal coordination   : angle       3.50716 (    9)
  covalent geometry    : bond        0.00307 (14864)
  covalent geometry    : angle       0.53575 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.078 
Fit side-chains
REVERT: A   58 THR cc_start: 0.9392 (p) cc_final: 0.9020 (p)
REVERT: B   63 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7675 (mt-10)
REVERT: G   74 LYS cc_start: 0.8650 (mttp) cc_final: 0.8190 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.3546
  time to fit residues: 56.0738
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0020
   chunk 49 optimal weight:    0.5980
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 110 optimal weight:    9.9990
   overall best weight:    0.8390

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.170686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119875 restraints weight = 19307.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.33
r_work: 0.2930 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.0513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14874  Z= 0.160
  Angle     :  0.541   7.552  21368  Z= 0.319
  Chirality :  0.035   0.133   2419
  Planarity :  0.005   0.051   1688
  Dihedral  : 29.193 176.568   4332
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.31 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.27), residues: 983
  helix:  1.83 (0.21), residues: 631
  sheet:  0.61 (1.00), residues: 24
  loop : -0.80 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.006   0.001   HIS L  75 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.009   0.001   TYR G  50 
 ARG   0.006   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00074 (    2)
  link_TRANS           : angle       0.32679 (    6)
  hydrogen bonds       : bond        0.04955 (  803)
  hydrogen bonds       : angle       2.98032 ( 2033)
  metal coordination   : bond        0.01364 (    8)
  metal coordination   : angle       4.36916 (    9)
  covalent geometry    : bond        0.00356 (14864)
  covalent geometry    : angle       0.53400 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9407 (p) cc_final: 0.9117 (p)
REVERT: B   63 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8166 (mt-10)
REVERT: E   59 GLU cc_start: 0.8620 (pt0) cc_final: 0.8381 (pt0)
REVERT: G   74 LYS cc_start: 0.8796 (mttp) cc_final: 0.8321 (mmtm)
  outliers start: 4
  outliers final: 4
  residues processed: 112
  average time/residue: 0.3480
  time to fit residues: 52.9201
Evaluate side-chains
  106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain K residue   49 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.9482

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.154510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.105181 restraints weight = 20839.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.42
r_work: 0.2760 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2607 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.0653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14874  Z= 0.163
  Angle     :  0.536   6.942  21368  Z= 0.316
  Chirality :  0.035   0.131   2419
  Planarity :  0.004   0.048   1688
  Dihedral  : 29.174 176.655   4332
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  8.29 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.27), residues: 983
  helix:  1.89 (0.21), residues: 633
  sheet:  0.62 (1.00), residues: 24
  loop : -0.83 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K  77 
 HIS   0.007   0.001   HIS L  75 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.008   0.001   TYR D  40 
 ARG   0.006   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00072 (    2)
  link_TRANS           : angle       0.44748 (    6)
  hydrogen bonds       : bond        0.04832 (  803)
  hydrogen bonds       : angle       2.89178 ( 2033)
  metal coordination   : bond        0.01351 (    8)
  metal coordination   : angle       4.12784 (    9)
  covalent geometry    : bond        0.00368 (14864)
  covalent geometry    : angle       0.52965 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8541 (mt-10)
REVERT: B   63 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8179 (mt-10)
REVERT: G   74 LYS cc_start: 0.8813 (mttp) cc_final: 0.8338 (mmtm)
  outliers start: 9
  outliers final: 6
  residues processed: 103
  average time/residue: 0.3567
  time to fit residues: 49.9231
Evaluate side-chains
  107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 91 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.169665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.119754 restraints weight = 25905.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.62
r_work: 0.3026 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.0675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  14874  Z= 0.152
  Angle     :  0.529   7.114  21368  Z= 0.313
  Chirality :  0.034   0.145   2419
  Planarity :  0.004   0.058   1688
  Dihedral  : 29.165 176.633   4332
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.28 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.27), residues: 983
  helix:  1.96 (0.21), residues: 633
  sheet:  0.64 (1.01), residues: 24
  loop : -0.82 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 
 PHE   0.017   0.001   PHE L  56 
 TYR   0.008   0.001   TYR D  40 
 ARG   0.004   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00034 (    2)
  link_TRANS           : angle       0.44269 (    6)
  hydrogen bonds       : bond        0.04706 (  803)
  hydrogen bonds       : angle       2.87933 ( 2033)
  metal coordination   : bond        0.01210 (    8)
  metal coordination   : angle       4.00268 (    9)
  covalent geometry    : bond        0.00341 (14864)
  covalent geometry    : angle       0.52262 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: B   63 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8096 (mt-10)
REVERT: G   74 LYS cc_start: 0.8760 (mttp) cc_final: 0.8275 (mmtm)
  outliers start: 7
  outliers final: 7
  residues processed: 110
  average time/residue: 0.3369
  time to fit residues: 50.1178
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 116 optimal weight:    0.6980
   chunk 109 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.168633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.120114 restraints weight = 24962.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.70
r_work: 0.2842 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14874  Z= 0.174
  Angle     :  0.542   6.674  21368  Z= 0.319
  Chirality :  0.035   0.133   2419
  Planarity :  0.004   0.049   1688
  Dihedral  : 29.228 176.787   4332
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.16 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.27), residues: 983
  helix:  1.95 (0.21), residues: 633
  sheet:  0.40 (0.99), residues: 24
  loop : -0.88 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.006   0.001   HIS L  75 
 PHE   0.029   0.002   PHE L  56 
 TYR   0.008   0.001   TYR D  40 
 ARG   0.006   0.000   ARG K  55 

Details of bonding type rmsd
  link_TRANS           : bond        0.00009 (    2)
  link_TRANS           : angle       0.45773 (    6)
  hydrogen bonds       : bond        0.04965 (  803)
  hydrogen bonds       : angle       2.85654 ( 2033)
  metal coordination   : bond        0.01276 (    8)
  metal coordination   : angle       4.02208 (    9)
  covalent geometry    : bond        0.00401 (14864)
  covalent geometry    : angle       0.53564 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: B   63 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8067 (mt-10)
REVERT: G   74 LYS cc_start: 0.8820 (mttp) cc_final: 0.8315 (mmtm)
REVERT: H   86 ARG cc_start: 0.8335 (mmt-90) cc_final: 0.7807 (mmt180)
REVERT: L    6 ILE cc_start: 0.6974 (mm) cc_final: 0.6686 (mm)
  outliers start: 17
  outliers final: 12
  residues processed: 106
  average time/residue: 0.3373
  time to fit residues: 48.8135
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   54 ILE
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  105 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 120 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   chunk 36 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.163496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.116413 restraints weight = 25292.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.66
r_work: 0.2902 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.0790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14874  Z= 0.149
  Angle     :  0.532   7.012  21368  Z= 0.315
  Chirality :  0.034   0.136   2419
  Planarity :  0.005   0.072   1688
  Dihedral  : 29.222 176.631   4332
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.86 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.27), residues: 983
  helix:  2.01 (0.21), residues: 633
  sheet:  0.42 (0.99), residues: 24
  loop : -0.86 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.014   0.001   PHE L  56 
 TYR   0.009   0.001   TYR D  40 
 ARG   0.006   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00014 (    2)
  link_TRANS           : angle       0.43663 (    6)
  hydrogen bonds       : bond        0.04740 (  803)
  hydrogen bonds       : angle       2.85976 ( 2033)
  metal coordination   : bond        0.01184 (    8)
  metal coordination   : angle       3.92780 (    9)
  covalent geometry    : bond        0.00331 (14864)
  covalent geometry    : angle       0.52613 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 1.816 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8313 (mt-10)
REVERT: B   63 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: G   74 LYS cc_start: 0.8781 (mttp) cc_final: 0.8290 (mmtm)
REVERT: H   86 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7782 (mmt180)
REVERT: L    6 ILE cc_start: 0.7070 (mm) cc_final: 0.6777 (mm)
  outliers start: 13
  outliers final: 12
  residues processed: 103
  average time/residue: 0.3802
  time to fit residues: 54.2276
Evaluate side-chains
  110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   54 ILE
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.0370
   chunk 40 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.7862

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.163710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.116797 restraints weight = 26086.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.71
r_work: 0.3062 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.0802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.154
  Angle     :  0.532   6.660  21368  Z= 0.314
  Chirality :  0.035   0.136   2419
  Planarity :  0.005   0.095   1688
  Dihedral  : 29.214 176.772   4332
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.75 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.27), residues: 983
  helix:  2.00 (0.21), residues: 634
  sheet:  0.43 (0.99), residues: 24
  loop : -0.86 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.003   0.001   HIS L  75 
 PHE   0.011   0.001   PHE L  56 
 TYR   0.008   0.001   TYR D  40 
 ARG   0.007   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00053 (    2)
  link_TRANS           : angle       0.39501 (    6)
  hydrogen bonds       : bond        0.04744 (  803)
  hydrogen bonds       : angle       2.84203 ( 2033)
  metal coordination   : bond        0.01129 (    8)
  metal coordination   : angle       3.88888 (    9)
  covalent geometry    : bond        0.00345 (14864)
  covalent geometry    : angle       0.52596 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8358 (mt-10)
REVERT: B   63 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: G   74 LYS cc_start: 0.8771 (mttp) cc_final: 0.8286 (mmtm)
REVERT: H   86 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.7812 (mmt180)
REVERT: L    6 ILE cc_start: 0.7007 (mm) cc_final: 0.6710 (mm)
  outliers start: 14
  outliers final: 13
  residues processed: 104
  average time/residue: 0.3352
  time to fit residues: 47.7793
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   54 ILE
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  105 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.163321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.116413 restraints weight = 25211.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.66
r_work: 0.2899 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.0867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14874  Z= 0.169
  Angle     :  0.537   7.020  21368  Z= 0.316
  Chirality :  0.035   0.136   2419
  Planarity :  0.004   0.048   1688
  Dihedral  : 29.230 176.866   4332
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.10 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.27), residues: 983
  helix:  1.99 (0.21), residues: 634
  sheet:  0.50 (1.00), residues: 24
  loop : -0.89 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.005   0.001   HIS L  75 
 PHE   0.020   0.001   PHE L  56 
 TYR   0.008   0.001   TYR D  40 
 ARG   0.005   0.000   ARG K  55 

Details of bonding type rmsd
  link_TRANS           : bond        0.00074 (    2)
  link_TRANS           : angle       0.56587 (    6)
  hydrogen bonds       : bond        0.04853 (  803)
  hydrogen bonds       : angle       2.82541 ( 2033)
  metal coordination   : bond        0.01290 (    8)
  metal coordination   : angle       3.93255 (    9)
  covalent geometry    : bond        0.00385 (14864)
  covalent geometry    : angle       0.53125 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8347 (mt-10)
REVERT: B   63 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: C   92 GLU cc_start: 0.8976 (mp0) cc_final: 0.8399 (mt-10)
REVERT: G   74 LYS cc_start: 0.8841 (mttp) cc_final: 0.8367 (mmtm)
REVERT: H   86 ARG cc_start: 0.8343 (mmt-90) cc_final: 0.8034 (mmt-90)
REVERT: L   83 SER cc_start: 0.7521 (t) cc_final: 0.7096 (p)
  outliers start: 14
  outliers final: 11
  residues processed: 105
  average time/residue: 0.3453
  time to fit residues: 49.7916
Evaluate side-chains
  110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  105 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0870
   chunk 106 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 86 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.163469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.120126 restraints weight = 31913.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.23
r_work: 0.2788 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14874  Z= 0.163
  Angle     :  0.538   7.970  21368  Z= 0.316
  Chirality :  0.035   0.143   2419
  Planarity :  0.004   0.048   1688
  Dihedral  : 29.229 176.847   4332
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.80 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.27), residues: 983
  helix:  2.03 (0.21), residues: 632
  sheet:  0.51 (1.00), residues: 24
  loop : -0.89 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 
 PHE   0.017   0.001   PHE L  56 
 TYR   0.008   0.001   TYR D  40 
 ARG   0.006   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00012 (    2)
  link_TRANS           : angle       0.51683 (    6)
  hydrogen bonds       : bond        0.04807 (  803)
  hydrogen bonds       : angle       2.82104 ( 2033)
  metal coordination   : bond        0.01239 (    8)
  metal coordination   : angle       3.89803 (    9)
  covalent geometry    : bond        0.00370 (14864)
  covalent geometry    : angle       0.53188 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8478 (mt-10)
REVERT: B   63 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8090 (mt-10)
REVERT: C   92 GLU cc_start: 0.9017 (mp0) cc_final: 0.8451 (mt-10)
REVERT: G   74 LYS cc_start: 0.8711 (mttp) cc_final: 0.8208 (mmtm)
REVERT: H   86 ARG cc_start: 0.8346 (mmt-90) cc_final: 0.8051 (mmt-90)
REVERT: L   83 SER cc_start: 0.7460 (t) cc_final: 0.7008 (p)
  outliers start: 11
  outliers final: 11
  residues processed: 103
  average time/residue: 0.3898
  time to fit residues: 55.0034
Evaluate side-chains
  109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  105 SER
Chi-restraints excluded: chain L residue  111 ASP
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0770
   chunk 27 optimal weight:    0.0970
   chunk 117 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.164147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118410 restraints weight = 35565.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.84
r_work: 0.2789 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.139
  Angle     :  0.530   7.995  21368  Z= 0.313
  Chirality :  0.034   0.138   2419
  Planarity :  0.004   0.060   1688
  Dihedral  : 29.221 176.685   4332
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.92 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.27), residues: 983
  helix:  2.07 (0.21), residues: 633
  sheet:  0.52 (1.00), residues: 24
  loop : -0.88 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.005   0.001   HIS L  75 
 PHE   0.016   0.001   PHE L  56 
 TYR   0.009   0.001   TYR D  40 
 ARG   0.020   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00029 (    2)
  link_TRANS           : angle       0.52707 (    6)
  hydrogen bonds       : bond        0.04601 (  803)
  hydrogen bonds       : angle       2.81420 ( 2033)
  metal coordination   : bond        0.01214 (    8)
  metal coordination   : angle       3.83182 (    9)
  covalent geometry    : bond        0.00293 (14864)
  covalent geometry    : angle       0.52428 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8643 (tt0) cc_final: 0.8366 (tt0)
REVERT: A   94 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8501 (mt-10)
REVERT: B   63 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8114 (mt-10)
REVERT: G   74 LYS cc_start: 0.8807 (mttp) cc_final: 0.8294 (mmtm)
REVERT: H   86 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.8031 (mmt-90)
REVERT: L   83 SER cc_start: 0.7371 (t) cc_final: 0.6919 (p)
  outliers start: 12
  outliers final: 11
  residues processed: 105
  average time/residue: 0.3287
  time to fit residues: 47.3858
Evaluate side-chains
  110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  105 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 104 optimal weight:    0.0970
   chunk 107 optimal weight:    0.8980
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.169628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.120474 restraints weight = 20095.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.43
r_work: 0.2929 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090  14874  Z= 0.148
  Angle     :  0.533   8.111  21368  Z= 0.314
  Chirality :  0.034   0.138   2419
  Planarity :  0.005   0.078   1688
  Dihedral  : 29.215 176.840   4332
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.15 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.27), residues: 983
  helix:  2.09 (0.21), residues: 631
  sheet:  0.51 (1.01), residues: 24
  loop : -0.87 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 
 PHE   0.023   0.001   PHE L  56 
 TYR   0.008   0.001   TYR D  40 
 ARG   0.015   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00074 (    2)
  link_TRANS           : angle       0.49078 (    6)
  hydrogen bonds       : bond        0.04619 (  803)
  hydrogen bonds       : angle       2.80541 ( 2033)
  metal coordination   : bond        0.01222 (    8)
  metal coordination   : angle       3.81389 (    9)
  covalent geometry    : bond        0.00335 (14864)
  covalent geometry    : angle       0.52714 (21353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7067.33 seconds
wall clock time: 122 minutes 35.41 seconds (7355.41 seconds total)