Starting phenix.real_space_refine
on Thu May 15 20:42:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn0_40608/05_2025/8sn0_40608.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn0_40608/05_2025/8sn0_40608.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn0_40608/05_2025/8sn0_40608.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn0_40608/05_2025/8sn0_40608.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn0_40608/05_2025/8sn0_40608.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn0_40608/05_2025/8sn0_40608.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.120
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7886      2.51       5
     N    2605      2.21       5
     O    3170      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13989
  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: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 682
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 3
    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      33.133  68.087  45.798  1.00 30.76           S
  ATOM  12446  SG  CYS K  51      33.688  64.517  44.566  1.00 32.93           S
  ATOM  12470  SG  CYS K  54      33.196  67.190  42.087  1.00 33.86           S
  ATOM  12187  SG  CYS K  16      23.428  61.844  52.457  1.00 53.78           S
  ATOM  12205  SG  CYS K  19      21.803  59.154  54.554  1.00 59.20           S
  ATOM  12335  SG  CYS K  36      24.773  60.893  56.009  1.00 41.49           S
  ATOM  12357  SG  CYS K  39      25.149  58.405  53.280  1.00 41.62           S

  Time building chain proxies: 8.87, per 1000 atoms: 0.63
  Number of scatterers: 13989
  At special positions: 0
  Unit cell: (108.896, 128.816, 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    3170      8.00
     N    2605      7.00
     C    7886      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: 3.32
  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  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      64.5% alpha, 4.7% beta
      136 base pairs and 250 stacking pairs defined.
    Time for finding SS restraints: 6.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.548A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.590A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 4.021A  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: 3.873A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.724A  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: 3.701A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.765A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.588A  pdb=" N   ASN C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.996A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU D  80 " --> pdb=" O   GLU D  76 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA D  81 " --> pdb=" O   ALA D  77 " (cutoff:3.500A)
      removed outlier: 3.947A  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 105 through 123
      removed outlier: 3.688A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   VAL D 111 " --> pdb=" O   ALA D 107 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 56
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.618A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.537A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.553A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.221A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.630A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 89
    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: 3.524A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.684A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 68
      removed outlier: 3.818A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.862A  pdb=" N   LYS K  82 " --> pdb=" O   THR K  78 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   HIS K  83 " --> pdb=" O   ILE K  79 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.535A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG K  91 " --> pdb=" O   GLU K  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.582A  pdb=" N   ALA L 107 " --> pdb=" O   LEU L 103 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.516A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 3.672A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ARG L 136 " --> pdb=" O   ASP L 132 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   ILE L 137 " --> pdb=" O   LYS L 133 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.995A  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: 7.205A  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
      removed outlier: 6.635A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.261A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.739A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25

    457 hydrogen bonds defined for protein.
    1354 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      250 stacking parallelities
  Total time for adding SS restraints: 5.12

  Time building geometry restraints manager: 3.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2898
        1.33 -     1.45: 4518
        1.45 -     1.57: 6805
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 14854
  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 1.72e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.57e+00
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.11e+00
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 8.66e-01
  bond pdb=" CG  LEU E 109 "
       pdb=" CD1 LEU E 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.18e-01
  ... (remaining 14849 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 20925
        1.76 -     3.52: 388
        3.52 -     5.27: 20
        5.27 -     7.03: 3
        7.03 -     8.79: 2
  Bond angle restraints: 21338
  Sorted by residual:
  angle pdb=" CB  ARG L 139 "
        pdb=" CG  ARG L 139 "
        pdb=" CD  ARG L 139 "
      ideal   model   delta    sigma   weight residual
     111.30  120.09   -8.79 2.30e+00 1.89e-01 1.46e+01
  angle pdb=" N   VAL E  46 "
        pdb=" CA  VAL E  46 "
        pdb=" C   VAL E  46 "
      ideal   model   delta    sigma   weight residual
     113.39  108.14    5.25 1.47e+00 4.63e-01 1.28e+01
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     122.82  126.95   -4.13 1.42e+00 4.96e-01 8.46e+00
  angle pdb=" N   GLN L 143 "
        pdb=" CA  GLN L 143 "
        pdb=" CB  GLN L 143 "
      ideal   model   delta    sigma   weight residual
     110.28  114.54   -4.26 1.55e+00 4.16e-01 7.57e+00
  angle pdb=" CA  VAL E  46 "
        pdb=" C   VAL E  46 "
        pdb=" N   ALA E  47 "
      ideal   model   delta    sigma   weight residual
     118.55  116.54    2.01 8.60e-01 1.35e+00 5.46e+00
  ... (remaining 21333 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 6813
       35.27 -    70.54: 1379
       70.54 -   105.81: 27
      105.81 -   141.08: 0
      141.08 -   176.35: 2
  Dihedral angle restraints: 8221
    sinusoidal: 5301
      harmonic: 2920
  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   66.81  153.19     1      3.50e+01 8.16e-04 1.48e+01
  dihedral pdb=" CA  LYS K  46 "
           pdb=" C   LYS K  46 "
           pdb=" N   ALA K  47 "
           pdb=" CA  ALA K  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.69  -18.31     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 8218 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1592
       0.030 -    0.060: 598
       0.060 -    0.089: 159
       0.089 -    0.119: 55
       0.119 -    0.149: 13
  Chirality restraints: 2417
  Sorted by residual:
  chirality pdb=" CA  ARG L 139 "
            pdb=" N   ARG L 139 "
            pdb=" C   ARG L 139 "
            pdb=" CB  ARG L 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  VAL K  27 "
            pdb=" N   VAL K  27 "
            pdb=" C   VAL K  27 "
            pdb=" CB  VAL K  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 2414 not shown)

  Planarity restraints: 1688
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.85e+00
        pdb=" N   PRO D 103 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR K  84 "    0.030 5.00e-02 4.00e+02   4.53e-02 3.29e+00
        pdb=" N   PRO K  85 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO K  85 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO K  85 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.025 2.00e-02 2.50e+03   1.04e-02 3.24e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1685 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 688
        2.72 -     3.26: 12175
        3.26 -     3.81: 24802
        3.81 -     4.35: 31855
        4.35 -     4.90: 46731
  Nonbonded interactions: 116251
  Sorted by model distance:
  nonbonded pdb=" O   ARG L 139 "
            pdb=" OG1 THR L 142 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.215 2.496
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" OG  SER K  60 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" NH2 ARG K  55 "
            pdb=" O   GLN L  92 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.263 3.120
  ... (remaining 116246 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=0.50 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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     39.950
  Find NCS groups from input model:        0.360
  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:             0.010
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
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      :  0.004   0.039  14864  Z= 0.162
  Angle     :  0.564   8.792  21353  Z= 0.331
  Chirality :  0.035   0.149   2417
  Planarity :  0.005   0.055   1686
  Dihedral  : 26.424 176.347   6329
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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:  1.04 (0.27), residues: 982
  helix:  1.58 (0.21), residues: 630
  sheet:  0.45 (0.99), residues: 24
  loop : -1.05 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 141 
 HIS   0.006   0.001   HIS C  31 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.021   0.001   TYR L 134 
 ARG   0.012   0.001   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00219 (    2)
  link_TRANS           : angle       0.53196 (    6)
  hydrogen bonds       : bond        0.11482 (  806)
  hydrogen bonds       : angle       4.01937 ( 2048)
  metal coordination   : bond        0.01153 (    8)
  metal coordination   : angle       4.09211 (    9)
  covalent geometry    : bond        0.00358 (14854)
  covalent geometry    : angle       0.55794 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9480 (p) cc_final: 0.9273 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.3633
  time to fit residues: 49.4493
Evaluate side-chains
  92 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 110 optimal weight:    7.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
H  47 GLN
L  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.149278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.113322 restraints weight = 18850.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.48
r_work: 0.2714 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.0694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14864  Z= 0.215
  Angle     :  0.596  10.043  21353  Z= 0.345
  Chirality :  0.038   0.153   2417
  Planarity :  0.005   0.054   1686
  Dihedral  : 29.497 176.163   4329
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.68 %
    Favored  : 92.50 %
  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:  1.12 (0.26), residues: 982
  helix:  1.67 (0.21), residues: 635
  sheet:  0.57 (1.00), residues: 24
  loop : -1.13 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K  61 
 HIS   0.007   0.001   HIS C  31 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.026   0.002   TYR L 134 
 ARG   0.005   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00016 (    2)
  link_TRANS           : angle       0.67039 (    6)
  hydrogen bonds       : bond        0.05874 (  806)
  hydrogen bonds       : angle       3.24730 ( 2048)
  metal coordination   : bond        0.00917 (    8)
  metal coordination   : angle       4.04228 (    9)
  covalent geometry    : bond        0.00498 (14854)
  covalent geometry    : angle       0.59054 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9512 (p) cc_final: 0.9307 (p)
REVERT: A  120 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7977 (mtt)
REVERT: G   74 LYS cc_start: 0.8209 (mptt) cc_final: 0.7934 (mmmm)
  outliers start: 7
  outliers final: 6
  residues processed: 98
  average time/residue: 0.3562
  time to fit residues: 47.1386
Evaluate side-chains
  99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue   73 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
H  47 GLN
L  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.152825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.112971 restraints weight = 26266.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.08
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.0705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14864  Z= 0.171
  Angle     :  0.567   9.705  21353  Z= 0.332
  Chirality :  0.036   0.140   2417
  Planarity :  0.005   0.052   1686
  Dihedral  : 29.476 175.870   4329
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 10.20 %
    Favored  : 89.21 %
  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:  1.29 (0.27), residues: 982
  helix:  1.83 (0.21), residues: 635
  sheet:  0.39 (0.98), residues: 24
  loop : -1.11 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.006   0.001   HIS C  31 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.026   0.001   TYR L 134 
 ARG   0.005   0.000   ARG E 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00081 (    2)
  link_TRANS           : angle       0.57241 (    6)
  hydrogen bonds       : bond        0.05374 (  806)
  hydrogen bonds       : angle       3.15159 ( 2048)
  metal coordination   : bond        0.00956 (    8)
  metal coordination   : angle       3.68482 (    9)
  covalent geometry    : bond        0.00385 (14854)
  covalent geometry    : angle       0.56237 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9516 (p) cc_final: 0.9304 (p)
REVERT: A  120 MET cc_start: 0.8193 (mtp) cc_final: 0.7963 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 94
  average time/residue: 0.3371
  time to fit residues: 43.5109
Evaluate side-chains
  95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.2980
   chunk 118 optimal weight:    0.9980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
K  83 HIS
L  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.150968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.112578 restraints weight = 25278.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.99
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.0852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14864  Z= 0.207
  Angle     :  0.581   9.662  21353  Z= 0.337
  Chirality :  0.037   0.143   2417
  Planarity :  0.005   0.051   1686
  Dihedral  : 29.566 176.032   4329
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.90 %
    Favored  : 87.81 %
  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:  1.31 (0.27), residues: 982
  helix:  1.86 (0.21), residues: 635
  sheet:  0.48 (0.97), residues: 24
  loop : -1.14 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K  61 
 HIS   0.005   0.001   HIS A 113 
 PHE   0.011   0.001   PHE B  61 
 TYR   0.026   0.002   TYR L 134 
 ARG   0.003   0.000   ARG F  45 

Details of bonding type rmsd
  link_TRANS           : bond        0.00050 (    2)
  link_TRANS           : angle       0.54473 (    6)
  hydrogen bonds       : bond        0.05641 (  806)
  hydrogen bonds       : angle       3.09697 ( 2048)
  metal coordination   : bond        0.00847 (    8)
  metal coordination   : angle       3.75323 (    9)
  covalent geometry    : bond        0.00481 (14854)
  covalent geometry    : angle       0.57572 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9528 (p) cc_final: 0.9315 (p)
REVERT: H  101 LEU cc_start: 0.8815 (mm) cc_final: 0.8606 (mm)
REVERT: L   38 MET cc_start: 0.6811 (tpp) cc_final: 0.6601 (mmm)
  outliers start: 11
  outliers final: 9
  residues processed: 95
  average time/residue: 0.3376
  time to fit residues: 43.6955
Evaluate side-chains
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue   73 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 121 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   overall best weight:    1.1184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.152329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.113269 restraints weight = 30329.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.36
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.0864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14864  Z= 0.179
  Angle     :  0.566   9.428  21353  Z= 0.331
  Chirality :  0.036   0.138   2417
  Planarity :  0.005   0.049   1686
  Dihedral  : 29.554 175.883   4329
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.72 %
    Favored  : 86.99 %
  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:  1.39 (0.27), residues: 982
  helix:  1.92 (0.21), residues: 635
  sheet:  0.44 (0.96), residues: 24
  loop : -1.10 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.026   0.001   TYR L 134 
 ARG   0.003   0.000   ARG E 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00047 (    2)
  link_TRANS           : angle       0.55287 (    6)
  hydrogen bonds       : bond        0.05374 (  806)
  hydrogen bonds       : angle       3.05888 ( 2048)
  metal coordination   : bond        0.00834 (    8)
  metal coordination   : angle       3.68027 (    9)
  covalent geometry    : bond        0.00408 (14854)
  covalent geometry    : angle       0.56115 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9519 (p) cc_final: 0.9296 (p)
REVERT: A  120 MET cc_start: 0.8132 (mtt) cc_final: 0.7891 (mtt)
  outliers start: 11
  outliers final: 9
  residues processed: 92
  average time/residue: 0.3305
  time to fit residues: 41.6309
Evaluate side-chains
  95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 120 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0870
   chunk 40 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   overall best weight:    1.7564

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.149708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.111048 restraints weight = 26394.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.16
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  14864  Z= 0.234
  Angle     :  0.602   9.947  21353  Z= 0.347
  Chirality :  0.039   0.136   2417
  Planarity :  0.005   0.050   1686
  Dihedral  : 29.689 175.712   4329
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.43 %
    Favored  : 85.93 %
  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:  1.20 (0.27), residues: 982
  helix:  1.78 (0.21), residues: 635
  sheet:  0.40 (0.93), residues: 24
  loop : -1.21 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K  61 
 HIS   0.005   0.001   HIS A 113 
 PHE   0.012   0.002   PHE A  78 
 TYR   0.029   0.002   TYR L 134 
 ARG   0.003   0.000   ARG H  92 

Details of bonding type rmsd
  link_TRANS           : bond        0.00075 (    2)
  link_TRANS           : angle       0.65632 (    6)
  hydrogen bonds       : bond        0.06035 (  806)
  hydrogen bonds       : angle       3.11464 ( 2048)
  metal coordination   : bond        0.00769 (    8)
  metal coordination   : angle       3.80619 (    9)
  covalent geometry    : bond        0.00551 (14854)
  covalent geometry    : angle       0.59744 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9527 (p) cc_final: 0.9302 (p)
REVERT: G   78 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8203 (mp)
  outliers start: 14
  outliers final: 11
  residues processed: 94
  average time/residue: 0.3449
  time to fit residues: 44.2564
Evaluate side-chains
  97 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue   73 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.151216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.112824 restraints weight = 20689.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.38
r_work: 0.2681 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14864  Z= 0.165
  Angle     :  0.576   9.942  21353  Z= 0.336
  Chirality :  0.037   0.137   2417
  Planarity :  0.005   0.050   1686
  Dihedral  : 29.652 174.884   4329
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.31 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.27), residues: 982
  helix:  1.96 (0.21), residues: 635
  sheet:  0.40 (0.94), residues: 24
  loop : -1.13 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.004   0.001   HIS C  31 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.026   0.001   TYR L 134 
 ARG   0.003   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00070 (    2)
  link_TRANS           : angle       0.58507 (    6)
  hydrogen bonds       : bond        0.05302 (  806)
  hydrogen bonds       : angle       3.05072 ( 2048)
  metal coordination   : bond        0.00883 (    8)
  metal coordination   : angle       3.77270 (    9)
  covalent geometry    : bond        0.00371 (14854)
  covalent geometry    : angle       0.57069 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9536 (p) cc_final: 0.9321 (p)
REVERT: E  131 ARG cc_start: 0.9107 (mtm180) cc_final: 0.8887 (mtm180)
REVERT: G   78 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8363 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 95
  average time/residue: 0.3322
  time to fit residues: 43.2133
Evaluate side-chains
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue   73 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 88 optimal weight:    4.9990
   chunk 108 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.151566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.112431 restraints weight = 19204.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.27
r_work: 0.2715 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14864  Z= 0.164
  Angle     :  0.567   9.167  21353  Z= 0.330
  Chirality :  0.036   0.135   2417
  Planarity :  0.005   0.048   1686
  Dihedral  : 29.611 175.684   4329
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.36 %
    Favored  : 85.35 %
  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:  1.50 (0.27), residues: 982
  helix:  2.02 (0.21), residues: 635
  sheet:  0.35 (0.94), residues: 24
  loop : -1.09 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.026   0.001   TYR L 134 
 ARG   0.006   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00037 (    2)
  link_TRANS           : angle       0.54319 (    6)
  hydrogen bonds       : bond        0.05238 (  806)
  hydrogen bonds       : angle       2.99238 ( 2048)
  metal coordination   : bond        0.00873 (    8)
  metal coordination   : angle       3.77475 (    9)
  covalent geometry    : bond        0.00368 (14854)
  covalent geometry    : angle       0.56135 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9531 (p) cc_final: 0.9315 (p)
REVERT: E  131 ARG cc_start: 0.9111 (mtm180) cc_final: 0.8889 (mtm180)
REVERT: G   78 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8353 (mp)
REVERT: L    1 MET cc_start: 0.5438 (tpt) cc_final: 0.4501 (ppp)
  outliers start: 11
  outliers final: 9
  residues processed: 97
  average time/residue: 0.3275
  time to fit residues: 43.6119
Evaluate side-chains
  100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue   73 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 116 optimal weight:    2.9990
   chunk 119 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.152382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.116929 restraints weight = 21758.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.85
r_work: 0.2745 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14864  Z= 0.171
  Angle     :  0.558   8.630  21353  Z= 0.325
  Chirality :  0.036   0.156   2417
  Planarity :  0.005   0.048   1686
  Dihedral  : 29.518 175.948   4329
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.13 %
    Favored  : 85.46 %
  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: 982
  helix:  2.10 (0.21), residues: 633
  sheet:  0.49 (0.95), residues: 24
  loop : -1.05 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.023   0.001   TYR L 134 
 ARG   0.005   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00049 (    2)
  link_TRANS           : angle       0.50055 (    6)
  hydrogen bonds       : bond        0.05012 (  806)
  hydrogen bonds       : angle       2.93703 ( 2048)
  metal coordination   : bond        0.00833 (    8)
  metal coordination   : angle       3.83571 (    9)
  covalent geometry    : bond        0.00388 (14854)
  covalent geometry    : angle       0.55271 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9530 (p) cc_final: 0.9318 (p)
REVERT: E  131 ARG cc_start: 0.9109 (mtm180) cc_final: 0.8880 (mtm180)
REVERT: G   78 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8327 (mp)
REVERT: G   92 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.7546 (mp0)
REVERT: L    1 MET cc_start: 0.5468 (tpt) cc_final: 0.4524 (ppp)
  outliers start: 12
  outliers final: 10
  residues processed: 99
  average time/residue: 0.3339
  time to fit residues: 45.5797
Evaluate side-chains
  100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   73 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.152866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.113687 restraints weight = 19500.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.20
r_work: 0.2745 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14864  Z= 0.158
  Angle     :  0.556  10.022  21353  Z= 0.324
  Chirality :  0.036   0.140   2417
  Planarity :  0.005   0.050   1686
  Dihedral  : 29.504 175.807   4329
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.01 %
    Favored  : 85.46 %
  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:  1.66 (0.27), residues: 982
  helix:  2.15 (0.21), residues: 633
  sheet:  0.56 (0.96), residues: 24
  loop : -1.02 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.022   0.001   TYR L 134 
 ARG   0.005   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00058 (    2)
  link_TRANS           : angle       0.49318 (    6)
  hydrogen bonds       : bond        0.04874 (  806)
  hydrogen bonds       : angle       2.93174 ( 2048)
  metal coordination   : bond        0.00854 (    8)
  metal coordination   : angle       3.84018 (    9)
  covalent geometry    : bond        0.00353 (14854)
  covalent geometry    : angle       0.55066 (21338)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9543 (p) cc_final: 0.9335 (p)
REVERT: E  131 ARG cc_start: 0.9108 (mtm180) cc_final: 0.8878 (mtm180)
REVERT: G   78 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8321 (mp)
REVERT: G   92 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.7578 (mp0)
REVERT: L    1 MET cc_start: 0.5422 (tpt) cc_final: 0.4533 (ppp)
  outliers start: 13
  outliers final: 10
  residues processed: 97
  average time/residue: 0.3241
  time to fit residues: 43.4765
Evaluate side-chains
  101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   73 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 117 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.152073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.114515 restraints weight = 20786.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.44
r_work: 0.2692 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14864  Z= 0.180
  Angle     :  0.566   9.363  21353  Z= 0.329
  Chirality :  0.037   0.152   2417
  Planarity :  0.005   0.048   1686
  Dihedral  : 29.519 176.047   4329
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.90 %
    Favored  : 85.46 %
  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:  1.59 (0.27), residues: 982
  helix:  2.08 (0.21), residues: 635
  sheet:  0.65 (0.97), residues: 24
  loop : -1.06 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.021   0.001   TYR L 134 
 ARG   0.005   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00050 (    2)
  link_TRANS           : angle       0.54718 (    6)
  hydrogen bonds       : bond        0.05198 (  806)
  hydrogen bonds       : angle       2.95662 ( 2048)
  metal coordination   : bond        0.00789 (    8)
  metal coordination   : angle       3.91715 (    9)
  covalent geometry    : bond        0.00413 (14854)
  covalent geometry    : angle       0.56039 (21338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5672.62 seconds
wall clock time: 98 minutes 44.05 seconds (5924.05 seconds total)