Starting phenix.real_space_refine
on Thu Jul 31 15:21:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn0_40608/07_2025/8sn0_40608.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn0_40608/07_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_40608/07_2025/8sn0_40608.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn0_40608/07_2025/8sn0_40608.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn0_40608/07_2025/8sn0_40608.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn0_40608/07_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-5711/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: 9.53, per 1000 atoms: 0.68
  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: 3.65
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  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: 7.11
  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: 5.04

  Time building geometry restraints manager: 4.36 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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     43.160
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.080
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.390
-------------------------------------------------------------------------------
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  : 1.033 
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: 0.3590
  time to fit residues: 49.2089
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  : 1.065 
-------------------------------------------------------------------------------
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 = 0.3521 r_free = 0.3521 target = 0.149165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.111419 restraints weight = 18832.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.36
r_work: 0.2658 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
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  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9527 (p) cc_final: 0.9325 (p)
REVERT: A  120 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8015 (mtt)
REVERT: G   74 LYS cc_start: 0.8252 (mptt) cc_final: 0.7992 (mmmm)
  outliers start: 7
  outliers final: 6
  residues processed: 98
  average time/residue: 0.3587
  time to fit residues: 47.3920
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  : 1.214 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 70 optimal weight:    0.0770
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.154409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.115201 restraints weight = 26220.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.15
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.0688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14864  Z= 0.142
  Angle     :  0.548   9.194  21353  Z= 0.325
  Chirality :  0.036   0.135   2417
  Planarity :  0.004   0.049   1686
  Dihedral  : 29.421 176.060   4329
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.85 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.27), residues: 982
  helix:  1.98 (0.21), residues: 635
  sheet:  0.39 (0.99), residues: 24
  loop : -1.03 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.004   0.001   HIS C  31 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.025   0.001   TYR L 134 
 ARG   0.003   0.000   ARG L  15 

Details of bonding type rmsd
  link_TRANS           : bond        0.00180 (    2)
  link_TRANS           : angle       0.39283 (    6)
  hydrogen bonds       : bond        0.04920 (  806)
  hydrogen bonds       : angle       3.06686 ( 2048)
  metal coordination   : bond        0.01275 (    8)
  metal coordination   : angle       3.63317 (    9)
  covalent geometry    : bond        0.00298 (14854)
  covalent geometry    : angle       0.54351 (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
  99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9498 (p) cc_final: 0.9282 (p)
  outliers start: 6
  outliers final: 4
  residues processed: 95
  average time/residue: 0.3396
  time to fit residues: 44.5921
Evaluate side-chains
  95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
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:    0.9990
   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:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 118 optimal weight:    0.6980
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.150904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.111137 restraints weight = 25332.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.03
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14864  Z= 0.231
  Angle     :  0.599   9.773  21353  Z= 0.346
  Chirality :  0.039   0.144   2417
  Planarity :  0.005   0.051   1686
  Dihedral  : 29.643 175.950   4329
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.90 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.27), residues: 982
  helix:  1.81 (0.21), residues: 635
  sheet:  0.41 (0.98), residues: 24
  loop : -1.17 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K  61 
 HIS   0.005   0.001   HIS A 113 
 PHE   0.012   0.002   PHE A  78 
 TYR   0.027   0.002   TYR L 134 
 ARG   0.003   0.000   ARG F  45 

Details of bonding type rmsd
  link_TRANS           : bond        0.00084 (    2)
  link_TRANS           : angle       0.63714 (    6)
  hydrogen bonds       : bond        0.06017 (  806)
  hydrogen bonds       : angle       3.15153 ( 2048)
  metal coordination   : bond        0.00779 (    8)
  metal coordination   : angle       3.75145 (    9)
  covalent geometry    : bond        0.00543 (14854)
  covalent geometry    : angle       0.59370 (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
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9531 (p) cc_final: 0.9306 (p)
REVERT: C   61 GLU cc_start: 0.8325 (tp30) cc_final: 0.7957 (tp30)
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 0.3359
  time to fit residues: 43.8133
Evaluate side-chains
  94 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
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   45 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain H residue   47 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 23 optimal weight:    0.2980
   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:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 105 optimal weight:    0.6980
   chunk 118 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.153810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.114886 restraints weight = 30296.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 2.39
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.0892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14864  Z= 0.147
  Angle     :  0.556   8.923  21353  Z= 0.327
  Chirality :  0.036   0.133   2417
  Planarity :  0.004   0.047   1686
  Dihedral  : 29.538 175.914   4329
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.08 %
    Favored  : 86.87 %
  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: 636
  sheet:  0.35 (0.98), residues: 24
  loop : -1.03 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.023   0.001   TYR L 134 
 ARG   0.003   0.000   ARG L 139 

Details of bonding type rmsd
  link_TRANS           : bond        0.00057 (    2)
  link_TRANS           : angle       0.43463 (    6)
  hydrogen bonds       : bond        0.04970 (  806)
  hydrogen bonds       : angle       2.98324 ( 2048)
  metal coordination   : bond        0.01186 (    8)
  metal coordination   : angle       3.69540 (    9)
  covalent geometry    : bond        0.00316 (14854)
  covalent geometry    : angle       0.55106 (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
  96 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9508 (p) cc_final: 0.9289 (p)
REVERT: C   61 GLU cc_start: 0.8253 (tp30) cc_final: 0.7945 (tp30)
REVERT: E  131 ARG cc_start: 0.9062 (mtm180) cc_final: 0.8861 (mtm180)
REVERT: G   78 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8147 (mp)
REVERT: L   38 MET cc_start: 0.6870 (tpp) cc_final: 0.6666 (mmm)
  outliers start: 9
  outliers final: 6
  residues processed: 91
  average time/residue: 0.3493
  time to fit residues: 43.5292
Evaluate side-chains
  92 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   47 GLN
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:    0.9980
   chunk 79 optimal weight:    4.9990
   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:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 121 optimal weight:    8.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.151749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.115407 restraints weight = 26372.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.41
r_work: 0.2632 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.0962

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= 0.188
  Angle     :  0.564   8.749  21353  Z= 0.329
  Chirality :  0.037   0.140   2417
  Planarity :  0.004   0.047   1686
  Dihedral  : 29.550 176.120   4329
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.01 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.27), residues: 982
  helix:  2.05 (0.21), residues: 635
  sheet:  0.35 (0.96), residues: 24
  loop : -1.07 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.026   0.002   TYR L 134 
 ARG   0.002   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.55392 (    6)
  hydrogen bonds       : bond        0.05298 (  806)
  hydrogen bonds       : angle       2.98312 ( 2048)
  metal coordination   : bond        0.00808 (    8)
  metal coordination   : angle       4.04803 (    9)
  covalent geometry    : bond        0.00434 (14854)
  covalent geometry    : angle       0.55826 (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
  101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9515 (p) cc_final: 0.9303 (p)
REVERT: E  131 ARG cc_start: 0.9127 (mtm180) cc_final: 0.8904 (mtm180)
REVERT: G   78 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8350 (mp)
  outliers start: 11
  outliers final: 10
  residues processed: 96
  average time/residue: 0.3365
  time to fit residues: 44.5549
Evaluate side-chains
  100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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 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:    1.9990
   chunk 53 optimal weight:    0.0970
   chunk 88 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.152339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.114047 restraints weight = 20739.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 1.46
r_work: 0.2687 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    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 = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.0964

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= 0.166
  Angle     :  0.560   9.058  21353  Z= 0.326
  Chirality :  0.036   0.155   2417
  Planarity :  0.004   0.046   1686
  Dihedral  : 29.538 175.888   4329
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.90 %
    Favored  : 85.58 %
  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:  2.09 (0.21), residues: 635
  sheet:  0.36 (0.97), residues: 24
  loop : -1.04 (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   0.009   0.001   PHE B  61 
 TYR   0.025   0.001   TYR L 134 
 ARG   0.003   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00052 (    2)
  link_TRANS           : angle       0.52540 (    6)
  hydrogen bonds       : bond        0.05074 (  806)
  hydrogen bonds       : angle       2.96187 ( 2048)
  metal coordination   : bond        0.00846 (    8)
  metal coordination   : angle       3.96427 (    9)
  covalent geometry    : bond        0.00373 (14854)
  covalent geometry    : angle       0.55397 (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
  100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9534 (p) cc_final: 0.9324 (p)
REVERT: E  131 ARG cc_start: 0.9105 (mtm180) cc_final: 0.8896 (mtm180)
REVERT: G   78 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8306 (mp)
REVERT: H   99 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8494 (ttm-80)
  outliers start: 13
  outliers final: 9
  residues processed: 94
  average time/residue: 0.3198
  time to fit residues: 41.8035
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  : 1.030 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.152620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.114422 restraints weight = 19254.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.20
r_work: 0.2704 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    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 = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.0967

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     :  0.557   8.474  21353  Z= 0.325
  Chirality :  0.036   0.140   2417
  Planarity :  0.004   0.050   1686
  Dihedral  : 29.528 176.067   4329
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.13 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.27), residues: 982
  helix:  2.12 (0.21), residues: 635
  sheet:  0.32 (0.96), residues: 24
  loop : -1.03 (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   0.009   0.001   PHE B  61 
 TYR   0.025   0.001   TYR L 134 
 ARG   0.003   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00056 (    2)
  link_TRANS           : angle       0.50295 (    6)
  hydrogen bonds       : bond        0.05039 (  806)
  hydrogen bonds       : angle       2.94173 ( 2048)
  metal coordination   : bond        0.00847 (    8)
  metal coordination   : angle       3.94557 (    9)
  covalent geometry    : bond        0.00373 (14854)
  covalent geometry    : angle       0.55090 (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
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9547 (p) cc_final: 0.9344 (p)
REVERT: E  131 ARG cc_start: 0.9111 (mtm180) cc_final: 0.8909 (mtm180)
REVERT: G   78 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8298 (mp)
  outliers start: 11
  outliers final: 10
  residues processed: 92
  average time/residue: 0.3396
  time to fit residues: 43.1724
Evaluate side-chains
  99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
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 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:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 116 optimal weight:    7.9990
   chunk 119 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.146901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.110812 restraints weight = 21822.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.82
r_work: 0.2696 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  14864  Z= 0.265
  Angle     :  0.624   9.786  21353  Z= 0.357
  Chirality :  0.040   0.138   2417
  Planarity :  0.005   0.048   1686
  Dihedral  : 29.763 175.726   4329
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  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:  1.22 (0.26), residues: 982
  helix:  1.82 (0.21), residues: 635
  sheet:  0.34 (0.94), residues: 24
  loop : -1.23 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K  61 
 HIS   0.006   0.001   HIS A 113 
 PHE   0.014   0.002   PHE A  78 
 TYR   0.026   0.002   TYR L 134 
 ARG   0.004   0.001   ARG G  81 

Details of bonding type rmsd
  link_TRANS           : bond        0.00114 (    2)
  link_TRANS           : angle       0.75148 (    6)
  hydrogen bonds       : bond        0.06406 (  806)
  hydrogen bonds       : angle       3.12077 ( 2048)
  metal coordination   : bond        0.00743 (    8)
  metal coordination   : angle       4.21463 (    9)
  covalent geometry    : bond        0.00631 (14854)
  covalent geometry    : angle       0.61796 (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
  101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9536 (p) cc_final: 0.9314 (p)
REVERT: G   78 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8342 (mp)
REVERT: G   92 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.7649 (mp0)
REVERT: H   99 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8428 (ttm-80)
  outliers start: 12
  outliers final: 10
  residues processed: 96
  average time/residue: 0.3450
  time to fit residues: 45.6040
Evaluate side-chains
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
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 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   73 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3580 r_free = 0.3580 target = 0.152975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.111003 restraints weight = 19541.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.21
r_work: 0.2714 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14864  Z= 0.150
  Angle     :  0.569   8.878  21353  Z= 0.334
  Chirality :  0.037   0.178   2417
  Planarity :  0.005   0.055   1686
  Dihedral  : 29.654 175.115   4329
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  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:  1.55 (0.27), residues: 982
  helix:  2.07 (0.21), residues: 634
  sheet:  0.45 (0.96), residues: 24
  loop : -1.09 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.024   0.001   TYR L 134 
 ARG   0.008   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00095 (    2)
  link_TRANS           : angle       0.49826 (    6)
  hydrogen bonds       : bond        0.05101 (  806)
  hydrogen bonds       : angle       2.97303 ( 2048)
  metal coordination   : bond        0.01383 (    8)
  metal coordination   : angle       4.15706 (    9)
  covalent geometry    : bond        0.00319 (14854)
  covalent geometry    : angle       0.56245 (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
  100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9553 (p) cc_final: 0.9344 (p)
REVERT: G   78 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8341 (mp)
REVERT: G   92 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.7616 (mp0)
  outliers start: 12
  outliers final: 8
  residues processed: 95
  average time/residue: 0.3273
  time to fit residues: 43.7746
Evaluate side-chains
  96 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
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 K residue   24 VAL
Chi-restraints excluded: chain K residue   60 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:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.3188

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.151207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.114441 restraints weight = 20855.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.58
r_work: 0.2718 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  14864  Z= 0.195
  Angle     :  0.578   9.559  21353  Z= 0.334
  Chirality :  0.037   0.167   2417
  Planarity :  0.005   0.052   1686
  Dihedral  : 29.592 175.583   4329
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.25 %
    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:  1.49 (0.27), residues: 982
  helix:  2.02 (0.21), residues: 635
  sheet:  0.43 (0.95), residues: 24
  loop : -1.12 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP K  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.022   0.001   TYR L 134 
 ARG   0.008   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00046 (    2)
  link_TRANS           : angle       0.55717 (    6)
  hydrogen bonds       : bond        0.05423 (  806)
  hydrogen bonds       : angle       2.99432 ( 2048)
  metal coordination   : bond        0.00818 (    8)
  metal coordination   : angle       4.27200 (    9)
  covalent geometry    : bond        0.00451 (14854)
  covalent geometry    : angle       0.57132 (21338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6482.01 seconds
wall clock time: 111 minutes 31.51 seconds (6691.51 seconds total)