Starting phenix.real_space_refine
on Mon May 19 10:46:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn1_40609/05_2025/8sn1_40609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn1_40609/05_2025/8sn1_40609.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn1_40609/05_2025/8sn1_40609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn1_40609/05_2025/8sn1_40609.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn1_40609/05_2025/8sn1_40609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn1_40609/05_2025/8sn1_40609.cif"
  }
  resolution = 3.3
  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=   0.107
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 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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      34.621  67.720  41.713  1.00 71.54           S
  ATOM  12446  SG  CYS K  51      32.912  64.309  42.021  1.00 58.73           S
  ATOM  12470  SG  CYS K  54      34.765  65.302  38.806  1.00 65.25           S
  ATOM  12187  SG  CYS K  16      21.868  63.309  48.158  1.00 77.69           S
  ATOM  12205  SG  CYS K  19      21.177  60.743  51.004  1.00 79.04           S
  ATOM  12335  SG  CYS K  36      23.454  63.950  51.370  1.00 71.93           S
  ATOM  12357  SG  CYS K  39      24.693  61.015  49.965  1.00 70.40           S

  Time building chain proxies: 8.48, per 1000 atoms: 0.61
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (110.224, 130.144, 124.832, 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: 3.05
  Conformation dependent library (CDL) restraints added in 1.2 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  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        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
      64.3% alpha, 4.4% beta
      135 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 6.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.564A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.585A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.924A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.877A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.591A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.659A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.693A  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: 3.558A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.782A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.535A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 3.983A  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: 3.822A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.624A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.678A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.782A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU E 126 " --> pdb=" O   LYS E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.744A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.898A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.573A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.522A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.642A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.613A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.764A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 3.674A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.766A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.772A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   HIS K  83 " --> pdb=" O   ILE K  79 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 86 through 91
      removed outlier: 4.374A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.718A  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 143
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.200A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.435A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.252A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
      removed outlier: 3.550A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24

    458 hydrogen bonds defined for protein.
    1356 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 4.90

  Time building geometry restraints manager: 3.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2909
        1.33 -     1.45: 4520
        1.45 -     1.57: 6802
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" CG1 ILE L  54 "
       pdb=" CD1 ILE L  54 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.34e+00
  bond pdb=" CG1 ILE H  54 "
       pdb=" CD1 ILE H  54 "
    ideal  model  delta    sigma   weight residual
    1.513  1.558 -0.045 3.90e-02 6.57e+02 1.33e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 9.58e-01
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 20384
        1.13 -     2.26: 820
        2.26 -     3.39: 127
        3.39 -     4.51: 8
        4.51 -     5.64: 14
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" C   ALA L  19 "
        pdb=" N   GLN L  20 "
        pdb=" CA  GLN L  20 "
      ideal   model   delta    sigma   weight residual
     121.54  126.24   -4.70 1.91e+00 2.74e-01 6.06e+00
  angle pdb=" CA  GLN L  20 "
        pdb=" CB  GLN L  20 "
        pdb=" CG  GLN L  20 "
      ideal   model   delta    sigma   weight residual
     114.10  118.63   -4.53 2.00e+00 2.50e-01 5.13e+00
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     122.46  125.47   -3.01 1.41e+00 5.03e-01 4.56e+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  118.22   -5.04 2.37e+00 1.78e-01 4.53e+00
  angle pdb=" C4'  DT J -17 "
        pdb=" C3'  DT J -17 "
        pdb=" C2'  DT J -17 "
      ideal   model   delta    sigma   weight residual
     102.40  105.43   -3.03 1.50e+00 4.44e-01 4.08e+00
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 6800
       35.27 -    70.54: 1406
       70.54 -   105.81: 22
      105.81 -   141.08: 0
      141.08 -   176.35: 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   43.65  176.35     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   70.74  149.26     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CB  GLU G  91 "
           pdb=" CG  GLU G  91 "
           pdb=" CD  GLU G  91 "
           pdb=" OE1 GLU G  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.86  -89.86     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1764
       0.034 -    0.067: 515
       0.067 -    0.101: 101
       0.101 -    0.134: 36
       0.134 -    0.168: 3
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.04e-01
  chirality pdb=" CA  VAL L  67 "
            pdb=" N   VAL L  67 "
            pdb=" C   VAL L  67 "
            pdb=" CB  VAL L  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  ILE H  54 "
            pdb=" N   ILE H  54 "
            pdb=" C   ILE H  54 "
            pdb=" CB  ILE H  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO L  61 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.025 2.00e-02 2.50e+03   1.09e-02 3.24e+00
        pdb=" N9   DA I -35 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.028 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO D 103 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2255
        2.78 -     3.31: 12147
        3.31 -     3.84: 25337
        3.84 -     4.37: 30734
        4.37 -     4.90: 44982
  Nonbonded interactions: 115455
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.273 2.496
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" N3   DC I  21 "
            pdb=" N1   DG J -21 "
     model   vdw
     2.318 2.560
  ... (remaining 115450 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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     38.060
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
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   0.045  14874  Z= 0.140
  Angle     :  0.542  12.165  21368  Z= 0.312
  Chirality :  0.034   0.168   2419
  Planarity :  0.004   0.047   1688
  Dihedral  : 26.479 176.350   6336
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.23 %
    Favored  : 99.65 %
  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:  1.60 (0.27), residues: 983
  helix:  2.10 (0.21), residues: 628
  sheet: -0.62 (1.11), residues: 24
  loop : -0.89 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP K  61 
 HIS   0.004   0.001   HIS C  82 
 PHE   0.010   0.001   PHE L  69 
 TYR   0.020   0.001   TYR C  50 
 ARG   0.003   0.000   ARG E 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00103 (    2)
  link_TRANS           : angle       0.45456 (    6)
  hydrogen bonds       : bond        0.10626 (  805)
  hydrogen bonds       : angle       3.65213 ( 2046)
  metal coordination   : bond        0.00657 (    8)
  metal coordination   : angle       6.93178 (    9)
  covalent geometry    : bond        0.00304 (14864)
  covalent geometry    : angle       0.52332 (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
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   99 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7258 (mtm180)
REVERT: E  122 LYS cc_start: 0.8891 (pttt) cc_final: 0.8580 (ptmt)
REVERT: E  129 ARG cc_start: 0.8628 (tmt170) cc_final: 0.8415 (tpt90)
REVERT: H   33 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7404 (mtt180)
REVERT: H   79 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8038 (mtm180)
REVERT: L  147 MET cc_start: 0.3445 (pmm) cc_final: 0.2318 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.3502
  time to fit residues: 49.4062
Evaluate side-chains
  87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.2980
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
K  41 GLN
K  65 HIS
L  46 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.155114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.108750 restraints weight = 21063.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.72
r_work: 0.2700 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    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 = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.0724

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= 0.184
  Angle     :  0.566  11.637  21368  Z= 0.326
  Chirality :  0.036   0.152   2419
  Planarity :  0.004   0.044   1688
  Dihedral  : 29.611 175.760   4332
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.37 %
    Favored  : 94.16 %
  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:  1.62 (0.27), residues: 983
  helix:  2.14 (0.21), residues: 632
  sheet: -0.72 (1.12), residues: 24
  loop : -0.95 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.012   0.001   TYR C  50 
 ARG   0.003   0.000   ARG A 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00044 (    2)
  link_TRANS           : angle       0.46667 (    6)
  hydrogen bonds       : bond        0.05525 (  805)
  hydrogen bonds       : angle       3.17537 ( 2046)
  metal coordination   : bond        0.00761 (    8)
  metal coordination   : angle       6.25298 (    9)
  covalent geometry    : bond        0.00426 (14864)
  covalent geometry    : angle       0.55176 (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
  93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9125 (mttm) cc_final: 0.8740 (mtpp)
REVERT: D   47 GLN cc_start: 0.8911 (mt0) cc_final: 0.8689 (mt0)
REVERT: D   99 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.7716 (mtm180)
REVERT: E  122 LYS cc_start: 0.9006 (pttt) cc_final: 0.8723 (ptmt)
REVERT: E  129 ARG cc_start: 0.8896 (tmt170) cc_final: 0.8536 (tpt90)
REVERT: G   73 ASN cc_start: 0.7977 (t0) cc_final: 0.7614 (t0)
REVERT: L    4 LYS cc_start: 0.8066 (mttt) cc_final: 0.7820 (mttp)
REVERT: L  147 MET cc_start: 0.3995 (pmm) cc_final: 0.2766 (mtt)
  outliers start: 3
  outliers final: 3
  residues processed: 92
  average time/residue: 0.3592
  time to fit residues: 44.5064
Evaluate side-chains
  89 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 120 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.155986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.109351 restraints weight = 21115.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.72
r_work: 0.2717 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.0731

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= 0.173
  Angle     :  0.550   9.993  21368  Z= 0.319
  Chirality :  0.035   0.147   2419
  Planarity :  0.004   0.044   1688
  Dihedral  : 29.596 175.709   4332
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.89 %
    Favored  : 92.52 %
  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:  2.10 (0.21), residues: 639
  sheet: -0.74 (1.11), residues: 24
  loop : -1.06 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.008   0.001   TYR H 121 
 ARG   0.007   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00092 (    2)
  link_TRANS           : angle       0.51294 (    6)
  hydrogen bonds       : bond        0.05325 (  805)
  hydrogen bonds       : angle       3.13401 ( 2046)
  metal coordination   : bond        0.00560 (    8)
  metal coordination   : angle       5.40599 (    9)
  covalent geometry    : bond        0.00394 (14864)
  covalent geometry    : angle       0.53912 (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
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9069 (mttm) cc_final: 0.8685 (mtpp)
REVERT: D   47 GLN cc_start: 0.8875 (mt0) cc_final: 0.8655 (mt0)
REVERT: D   99 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7639 (mtm180)
REVERT: E  122 LYS cc_start: 0.8981 (pttt) cc_final: 0.8688 (ptmt)
REVERT: E  129 ARG cc_start: 0.8839 (tmt170) cc_final: 0.8464 (tpt90)
REVERT: G   73 ASN cc_start: 0.7945 (t0) cc_final: 0.7538 (t0)
REVERT: L    4 LYS cc_start: 0.8069 (mttt) cc_final: 0.7793 (mttp)
REVERT: L   92 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7932 (mm-40)
REVERT: L  147 MET cc_start: 0.4020 (pmm) cc_final: 0.2798 (mtt)
  outliers start: 4
  outliers final: 3
  residues processed: 94
  average time/residue: 0.3481
  time to fit residues: 44.0026
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0770
   chunk 58 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.158185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.110030 restraints weight = 26473.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.41
r_work: 0.2639 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.0726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14874  Z= 0.144
  Angle     :  0.529   9.001  21368  Z= 0.310
  Chirality :  0.034   0.148   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.510 176.089   4332
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.59 %
    Favored  : 91.47 %
  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:  1.74 (0.27), residues: 983
  helix:  2.25 (0.21), residues: 639
  sheet: -0.67 (1.11), residues: 24
  loop : -1.01 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.008   0.001   PHE L  62 
 TYR   0.007   0.001   TYR F  51 
 ARG   0.004   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00097 (    2)
  link_TRANS           : angle       0.44496 (    6)
  hydrogen bonds       : bond        0.04805 (  805)
  hydrogen bonds       : angle       3.03165 ( 2046)
  metal coordination   : bond        0.00555 (    8)
  metal coordination   : angle       4.88906 (    9)
  covalent geometry    : bond        0.00314 (14864)
  covalent geometry    : angle       0.51972 (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
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9062 (mttm) cc_final: 0.8670 (mtpp)
REVERT: D   47 GLN cc_start: 0.8917 (mt0) cc_final: 0.8682 (mt0)
REVERT: D   99 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.7646 (mtm180)
REVERT: E  122 LYS cc_start: 0.8990 (pttt) cc_final: 0.8686 (pttt)
REVERT: E  129 ARG cc_start: 0.8866 (tmt170) cc_final: 0.8487 (tpt90)
REVERT: G   73 ASN cc_start: 0.7972 (t0) cc_final: 0.7565 (t0)
REVERT: H   59 MET cc_start: 0.8911 (tpp) cc_final: 0.8432 (mmm)
REVERT: L   92 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7912 (mm-40)
REVERT: L  147 MET cc_start: 0.4013 (pmm) cc_final: 0.2814 (mtt)
  outliers start: 7
  outliers final: 6
  residues processed: 99
  average time/residue: 0.3245
  time to fit residues: 43.6685
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   50 CYS
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 116 optimal weight:    8.9990
   chunk 109 optimal weight:   20.0000
   chunk 115 optimal weight:    8.9990
   chunk 61 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.154580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.106965 restraints weight = 25549.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.31
r_work: 0.2643 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.0904

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= 0.186
  Angle     :  0.554   9.292  21368  Z= 0.322
  Chirality :  0.036   0.151   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.665 175.349   4332
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.58 %
    Favored  : 89.49 %
  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:  1.54 (0.27), residues: 983
  helix:  2.09 (0.21), residues: 640
  sheet: -0.72 (1.11), residues: 24
  loop : -1.10 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.009   0.001   TYR H 121 
 ARG   0.005   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00040 (    2)
  link_TRANS           : angle       0.45969 (    6)
  hydrogen bonds       : bond        0.05466 (  805)
  hydrogen bonds       : angle       3.07469 ( 2046)
  metal coordination   : bond        0.00632 (    8)
  metal coordination   : angle       4.93673 (    9)
  covalent geometry    : bond        0.00432 (14864)
  covalent geometry    : angle       0.54513 (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
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9107 (mttm) cc_final: 0.8678 (mtpp)
REVERT: D   47 GLN cc_start: 0.8927 (mt0) cc_final: 0.8715 (mt0)
REVERT: D   99 ARG cc_start: 0.8422 (mtt-85) cc_final: 0.7618 (mtm180)
REVERT: E  122 LYS cc_start: 0.9020 (pttt) cc_final: 0.8715 (ptmt)
REVERT: E  129 ARG cc_start: 0.8898 (tmt170) cc_final: 0.8509 (tpt90)
REVERT: G   73 ASN cc_start: 0.8066 (t0) cc_final: 0.7676 (t0)
REVERT: H   59 MET cc_start: 0.8962 (tpp) cc_final: 0.8401 (mmm)
REVERT: L   92 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7927 (mm-40)
REVERT: L  147 MET cc_start: 0.3993 (pmm) cc_final: 0.2797 (mtt)
  outliers start: 7
  outliers final: 6
  residues processed: 98
  average time/residue: 0.3405
  time to fit residues: 45.3934
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   50 CYS
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 120 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.155453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.108887 restraints weight = 25889.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.58
r_work: 0.2589 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.0895

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= 0.169
  Angle     :  0.549   8.823  21368  Z= 0.319
  Chirality :  0.035   0.147   2419
  Planarity :  0.004   0.043   1688
  Dihedral  : 29.651 175.340   4332
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.28 %
    Favored  : 88.79 %
  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:  1.56 (0.27), residues: 983
  helix:  2.10 (0.21), residues: 640
  sheet: -0.84 (1.07), residues: 24
  loop : -1.08 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.010   0.001   PHE L  56 
 TYR   0.008   0.001   TYR H 121 
 ARG   0.007   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00196 (    2)
  link_TRANS           : angle       0.60108 (    6)
  hydrogen bonds       : bond        0.05278 (  805)
  hydrogen bonds       : angle       3.04810 ( 2046)
  metal coordination   : bond        0.00523 (    8)
  metal coordination   : angle       4.72427 (    9)
  covalent geometry    : bond        0.00388 (14864)
  covalent geometry    : angle       0.54085 (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
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9111 (mttm) cc_final: 0.8687 (mtpp)
REVERT: D   47 GLN cc_start: 0.8939 (mt0) cc_final: 0.8700 (mt0)
REVERT: D   99 ARG cc_start: 0.8449 (mtt-85) cc_final: 0.7626 (mtm180)
REVERT: E  122 LYS cc_start: 0.9060 (pttt) cc_final: 0.8756 (ptmt)
REVERT: E  129 ARG cc_start: 0.8903 (tmt170) cc_final: 0.8507 (tpt90)
REVERT: G   73 ASN cc_start: 0.8088 (t0) cc_final: 0.7668 (t0)
REVERT: H   59 MET cc_start: 0.8968 (tpp) cc_final: 0.8400 (mmm)
REVERT: L   38 MET cc_start: 0.5368 (mtm) cc_final: 0.4997 (mmm)
REVERT: L   52 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4190 (pp)
REVERT: L   92 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7911 (mm-40)
REVERT: L  147 MET cc_start: 0.4014 (pmm) cc_final: 0.2843 (mtt)
  outliers start: 7
  outliers final: 5
  residues processed: 99
  average time/residue: 0.3613
  time to fit residues: 48.5565
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   50 CYS
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.156263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.110353 restraints weight = 26621.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 2.66
r_work: 0.2611 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14874  Z= 0.149
  Angle     :  0.535   8.300  21368  Z= 0.314
  Chirality :  0.035   0.146   2419
  Planarity :  0.004   0.043   1688
  Dihedral  : 29.619 175.377   4332
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.51 %
    Favored  : 88.43 %
  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:  1.67 (0.27), residues: 983
  helix:  2.19 (0.21), residues: 640
  sheet: -0.71 (1.10), residues: 24
  loop : -1.05 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.019   0.001   PHE L  56 
 TYR   0.007   0.001   TYR F  51 
 ARG   0.009   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00053 (    2)
  link_TRANS           : angle       0.45276 (    6)
  hydrogen bonds       : bond        0.05009 (  805)
  hydrogen bonds       : angle       3.02041 ( 2046)
  metal coordination   : bond        0.00432 (    8)
  metal coordination   : angle       4.52491 (    9)
  covalent geometry    : bond        0.00330 (14864)
  covalent geometry    : angle       0.52706 (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
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9135 (mttm) cc_final: 0.8727 (mtpp)
REVERT: D   47 GLN cc_start: 0.8959 (mt0) cc_final: 0.8726 (mt0)
REVERT: D   99 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.7692 (mtm180)
REVERT: E  122 LYS cc_start: 0.9077 (pttt) cc_final: 0.8773 (ptmt)
REVERT: E  129 ARG cc_start: 0.8938 (tmt170) cc_final: 0.8625 (tpt90)
REVERT: G   73 ASN cc_start: 0.8083 (t0) cc_final: 0.7671 (t0)
REVERT: H   59 MET cc_start: 0.8964 (tpp) cc_final: 0.8414 (mmm)
REVERT: L   38 MET cc_start: 0.5235 (mtm) cc_final: 0.4993 (mmm)
REVERT: L   52 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.4198 (pp)
REVERT: L   92 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7941 (mm-40)
REVERT: L  147 MET cc_start: 0.4036 (pmm) cc_final: 0.2877 (mtt)
  outliers start: 8
  outliers final: 6
  residues processed: 100
  average time/residue: 0.3638
  time to fit residues: 49.4932
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   50 CYS
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.155250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.108704 restraints weight = 25619.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.51
r_work: 0.2572 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1006

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= 0.180
  Angle     :  0.548   9.315  21368  Z= 0.319
  Chirality :  0.036   0.150   2419
  Planarity :  0.004   0.043   1688
  Dihedral  : 29.651 174.920   4332
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.10 %
    Favored  : 87.73 %
  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:  2.12 (0.21), residues: 640
  sheet: -0.65 (1.13), residues: 24
  loop : -1.10 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.012   0.001   PHE L  56 
 TYR   0.009   0.001   TYR H 121 
 ARG   0.007   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00023 (    2)
  link_TRANS           : angle       0.57153 (    6)
  hydrogen bonds       : bond        0.05319 (  805)
  hydrogen bonds       : angle       3.02384 ( 2046)
  metal coordination   : bond        0.00617 (    8)
  metal coordination   : angle       4.77409 (    9)
  covalent geometry    : bond        0.00416 (14864)
  covalent geometry    : angle       0.53956 (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
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9103 (mttm) cc_final: 0.8729 (mtpp)
REVERT: D   47 GLN cc_start: 0.8960 (mt0) cc_final: 0.8728 (mt0)
REVERT: D   99 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.7664 (mtm180)
REVERT: E  129 ARG cc_start: 0.8879 (tmt170) cc_final: 0.8561 (tpt90)
REVERT: G   73 ASN cc_start: 0.8016 (t0) cc_final: 0.7553 (t0)
REVERT: H   59 MET cc_start: 0.8962 (tpp) cc_final: 0.8381 (mmm)
REVERT: L   52 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4333 (pp)
REVERT: L   92 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8013 (mm-40)
REVERT: L  147 MET cc_start: 0.3882 (pmm) cc_final: 0.2716 (mtt)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 0.3185
  time to fit residues: 44.1989
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   50 CYS
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   chunk 101 optimal weight:    0.5980
   chunk 116 optimal weight:    9.9990
   chunk 86 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.155984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.111257 restraints weight = 32408.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 3.19
r_work: 0.2566 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2517 r_free = 0.2517    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2517 r_free = 0.2517    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.0999

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= 0.151
  Angle     :  0.539   8.893  21368  Z= 0.315
  Chirality :  0.035   0.153   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.629 174.735   4332
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.10 %
    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:  1.68 (0.27), residues: 983
  helix:  2.21 (0.21), residues: 640
  sheet: -0.63 (1.13), residues: 24
  loop : -1.07 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.008   0.001   PHE L  56 
 TYR   0.007   0.001   TYR F  51 
 ARG   0.006   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00156 (    2)
  link_TRANS           : angle       0.50307 (    6)
  hydrogen bonds       : bond        0.05033 (  805)
  hydrogen bonds       : angle       3.00468 ( 2046)
  metal coordination   : bond        0.00510 (    8)
  metal coordination   : angle       4.68638 (    9)
  covalent geometry    : bond        0.00337 (14864)
  covalent geometry    : angle       0.53079 (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
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9071 (mttm) cc_final: 0.8702 (mtpp)
REVERT: D   47 GLN cc_start: 0.8967 (mt0) cc_final: 0.8735 (mt0)
REVERT: D   99 ARG cc_start: 0.8508 (mtt-85) cc_final: 0.7668 (mtm180)
REVERT: E  129 ARG cc_start: 0.8877 (tmt170) cc_final: 0.8556 (tpt90)
REVERT: G   73 ASN cc_start: 0.8001 (t0) cc_final: 0.7532 (t0)
REVERT: H   59 MET cc_start: 0.9040 (tpp) cc_final: 0.8489 (mmm)
REVERT: L   52 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.4159 (pp)
REVERT: L   92 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8003 (mm-40)
REVERT: L  147 MET cc_start: 0.3913 (pmm) cc_final: 0.2761 (mtt)
  outliers start: 10
  outliers final: 7
  residues processed: 100
  average time/residue: 0.3100
  time to fit residues: 42.9783
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   50 CYS
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
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:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.153244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.109323 restraints weight = 36430.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 3.32
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14874  Z= 0.206
  Angle     :  0.571   9.332  21368  Z= 0.331
  Chirality :  0.037   0.168   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.776 174.013   4332
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.45 %
    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:  1.46 (0.27), residues: 983
  helix:  2.05 (0.21), residues: 640
  sheet: -0.89 (1.10), residues: 24
  loop : -1.18 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.005   0.001   HIS E 113 
 PHE   0.011   0.002   PHE F  61 
 TYR   0.011   0.001   TYR H 121 
 ARG   0.007   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00048 (    2)
  link_TRANS           : angle       0.60551 (    6)
  hydrogen bonds       : bond        0.05784 (  805)
  hydrogen bonds       : angle       3.09038 ( 2046)
  metal coordination   : bond        0.00641 (    8)
  metal coordination   : angle       4.79517 (    9)
  covalent geometry    : bond        0.00486 (14864)
  covalent geometry    : angle       0.56306 (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
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8750 (mttm) cc_final: 0.8313 (mtpp)
REVERT: D   47 GLN cc_start: 0.8747 (mt0) cc_final: 0.8504 (mt0)
REVERT: D   99 ARG cc_start: 0.7723 (mtt-85) cc_final: 0.7168 (mtm180)
REVERT: E  129 ARG cc_start: 0.8595 (tmt170) cc_final: 0.8338 (tpt90)
REVERT: G   73 ASN cc_start: 0.7775 (t0) cc_final: 0.7296 (t0)
REVERT: H   59 MET cc_start: 0.8480 (tpp) cc_final: 0.7840 (mmm)
REVERT: L   52 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.3744 (pp)
REVERT: L   92 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7883 (mm-40)
REVERT: L  147 MET cc_start: 0.3469 (pmm) cc_final: 0.2165 (mtt)
  outliers start: 7
  outliers final: 6
  residues processed: 94
  average time/residue: 0.3292
  time to fit residues: 42.6754
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   50 CYS
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.155594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.107576 restraints weight = 20681.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.73
r_work: 0.2664 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14874  Z= 0.158
  Angle     :  0.552   8.965  21368  Z= 0.322
  Chirality :  0.036   0.160   2419
  Planarity :  0.004   0.043   1688
  Dihedral  : 29.721 173.923   4332
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.45 %
    Favored  : 87.50 %
  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:  2.14 (0.21), residues: 640
  sheet: -0.89 (1.11), residues: 24
  loop : -1.13 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.009   0.001   PHE L  56 
 TYR   0.007   0.001   TYR F  51 
 ARG   0.007   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00075 (    2)
  link_TRANS           : angle       0.51627 (    6)
  hydrogen bonds       : bond        0.05266 (  805)
  hydrogen bonds       : angle       3.04643 ( 2046)
  metal coordination   : bond        0.00522 (    8)
  metal coordination   : angle       4.70040 (    9)
  covalent geometry    : bond        0.00361 (14864)
  covalent geometry    : angle       0.54343 (21353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6046.86 seconds
wall clock time: 105 minutes 19.43 seconds (6319.43 seconds total)