Starting phenix.real_space_refine
on Thu Sep 18 05:10:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn4_40612/09_2025/8sn4_40612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn4_40612/09_2025/8sn4_40612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn4_40612/09_2025/8sn4_40612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn4_40612/09_2025/8sn4_40612.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn4_40612/09_2025/8sn4_40612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn4_40612/09_2025/8sn4_40612.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14600
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      33.347  72.273  47.031  1.00 86.22           S
  ATOM  12446  SG  CYS K  51      34.177  68.839  45.573  1.00 81.44           S
  ATOM  12470  SG  CYS K  54      33.180  71.557  43.284  1.00 91.27           S
  ATOM  12187  SG  CYS K  16      23.217  66.833  52.909  1.00107.40           S
  ATOM  12205  SG  CYS K  19      21.018  64.361  54.707  1.00109.20           S
  ATOM  12335  SG  CYS K  36      24.056  65.730  56.569  1.00 99.38           S
  ATOM  12357  SG  CYS K  39      24.585  63.331  53.903  1.00 91.82           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.74, per 1000 atoms: 0.26
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (111.552, 131.472, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      33     16.00
     P     294     15.00
     O    3289      8.00
     N    2713      7.00
     C    8269      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 575.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        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


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

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      63.5% alpha, 5.2% beta
      135 base pairs and 237 stacking pairs defined.
    Time for finding SS restraints: 2.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.624A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.634A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.864A  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: 3.996A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.664A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.642A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 83
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.624A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.709A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
      removed outlier: 3.766A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.835A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.512A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.744A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.559A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (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 90
      removed outlier: 3.536A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.581A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.730A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.933A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.567A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG K  91 " --> pdb=" O   GLU K  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.509A  pdb=" N   ARG L   5 " --> pdb=" O   MET L   1 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 86 through 91
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.581A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 131 through 147
      removed outlier: 4.138A  pdb=" N   ILE L 137 " --> pdb=" O   LYS L 133 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   GLN L 143 " --> pdb=" O   ARG L 139 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LYS L 144 " --> pdb=" O   GLU L 140 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 55 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.926A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.521A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.910A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.378A  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: 7.165A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28
      removed outlier: 3.578A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB3, first strand: chain 'M' and resid 12 through 16
      removed outlier: 9.416A  pdb=" N   LEU M  67 " --> pdb=" O   GLN M   2 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   PHE M   4 " --> pdb=" O   LEU M  67 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   LEU M  69 " --> pdb=" O   PHE M   4 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LYS M   6 " --> pdb=" O   LEU M  69 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   LEU M  71 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)

    495 hydrogen bonds defined for protein.
    1443 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      237 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3478
        1.34 -     1.46: 4329
        1.46 -     1.58: 7030
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" N   ASP A  81 "
       pdb=" CA  ASP A  81 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.29e-02 6.01e+03 1.96e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" CG  LEU E 126 "
       pdb=" CD1 LEU E 126 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.08e+00
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 1.04e+00
  bond pdb=" CG  LEU B  58 "
       pdb=" CD1 LEU B  58 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.48e-01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 21747
        1.85 -     3.69: 393
        3.69 -     5.54: 24
        5.54 -     7.39: 5
        7.39 -     9.23: 2
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" CA  ARG L 136 "
        pdb=" CB  ARG L 136 "
        pdb=" CG  ARG L 136 "
      ideal   model   delta    sigma   weight residual
     114.10  121.54   -7.44 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  127.70   -6.16 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" CA  LEU K  49 "
        pdb=" CB  LEU K  49 "
        pdb=" CG  LEU K  49 "
      ideal   model   delta    sigma   weight residual
     116.30  125.53   -9.23 3.50e+00 8.16e-02 6.96e+00
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     121.54  126.38   -4.84 1.91e+00 2.74e-01 6.43e+00
  angle pdb=" CB  LYS C 118 "
        pdb=" CG  LYS C 118 "
        pdb=" CD  LYS C 118 "
      ideal   model   delta    sigma   weight residual
     111.30  116.81   -5.51 2.30e+00 1.89e-01 5.73e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.62: 7271
       35.62 -    71.24: 1314
       71.24 -   106.86: 24
      106.86 -   142.48: 0
      142.48 -   178.10: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  Sorted by residual:
  dihedral pdb=" CA  ASP L  29 "
           pdb=" C   ASP L  29 "
           pdb=" N   MET L  30 "
           pdb=" CA  MET L  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.10 -178.10     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   74.08  145.92     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 2231
       0.052 -    0.105: 247
       0.105 -    0.157: 36
       0.157 -    0.209: 1
       0.209 -    0.262: 1
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CB  ILE L 137 "
            pdb=" CA  ILE L 137 "
            pdb=" CG1 ILE L 137 "
            pdb=" CG2 ILE L 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  ARG L 136 "
            pdb=" N   ARG L 136 "
            pdb=" C   ARG L 136 "
            pdb=" CB  ARG L 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.85e-01
  chirality pdb=" CA  ASP A  81 "
            pdb=" N   ASP A  81 "
            pdb=" C   ASP A  81 "
            pdb=" CB  ASP A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.04e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  33 "    0.017 2.00e-02 2.50e+03   1.41e-02 4.96e+00
        pdb=" CG  TRP L  33 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  33 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  33 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  33 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  33 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  33 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  33 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  33 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K  37 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO K  38 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO K  38 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO K  38 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO A  43 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 421
        2.69 -     3.24: 13054
        3.24 -     3.79: 26064
        3.79 -     4.35: 32194
        4.35 -     4.90: 47740
  Nonbonded interactions: 119473
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.136 2.496
  nonbonded pdb=" O   ASP L  87 "
            pdb=" OG  SER L  91 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" ND2 ASN A 108 "
            pdb=" O   GLY B  42 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OG  SER D  64 "
            pdb=" O   GLY F 101 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER L  91 "
            pdb=" OE1 GLN L  92 "
     model   vdw
     2.237 3.040
  ... (remaining 119468 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.17 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.910
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15482  Z= 0.145
  Angle     :  0.557   9.232  22186  Z= 0.321
  Chirality :  0.034   0.262   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 25.751 178.102   6577
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.26), residues: 1057
  helix:  2.28 (0.21), residues: 643
  sheet:  1.82 (0.76), residues: 48
  loop : -0.85 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L 136 
 TYR   0.022   0.001   TYR H  40 
 PHE   0.009   0.001   PHE D  65 
 TRP   0.038   0.003   TRP L  33 
 HIS   0.007   0.001   HIS L  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (15472)
  covalent geometry    : angle       0.55170 (22171)
  hydrogen bonds       : bond        0.10682 (  842)
  hydrogen bonds       : angle       4.11058 ( 2133)
  metal coordination   : bond        0.01850 (    8)
  metal coordination   : angle       3.84400 (    9)
  link_TRANS           : bond        0.00188 (    2)
  link_TRANS           : angle       0.45399 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.8469 (m110) cc_final: 0.8112 (m110)
REVERT: C   11 SER cc_start: 0.8505 (t) cc_final: 0.8201 (p)
REVERT: D   40 TYR cc_start: 0.9159 (m-80) cc_final: 0.8378 (m-80)
REVERT: D   51 ASP cc_start: 0.7966 (p0) cc_final: 0.7740 (p0)
REVERT: F   74 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7890 (tm-30)
REVERT: L    7 ASN cc_start: 0.9106 (m-40) cc_final: 0.8813 (m110)
REVERT: M    1 MET cc_start: 0.8023 (tmm) cc_final: 0.7345 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1625
  time to fit residues: 47.4289
Evaluate side-chains
  164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  83 HIS
M   2 GLN
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.137325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.078753 restraints weight = 42034.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.080995 restraints weight = 22779.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.082471 restraints weight = 16097.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.083273 restraints weight = 13438.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.083634 restraints weight = 12323.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  15482  Z= 0.299
  Angle     :  0.672  11.973  22186  Z= 0.376
  Chirality :  0.041   0.188   2516
  Planarity :  0.006   0.052   1794
  Dihedral  : 28.987 176.642   4413
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.82 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.26), residues: 1057
  helix:  2.00 (0.20), residues: 650
  sheet:  1.86 (0.77), residues: 53
  loop : -0.97 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  86 
 TYR   0.028   0.002   TYR H  40 
 PHE   0.015   0.002   PHE L  50 
 TRP   0.038   0.004   TRP L  33 
 HIS   0.009   0.001   HIS K  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 (15472)
  covalent geometry    : angle       0.66066 (22171)
  hydrogen bonds       : bond        0.06012 (  842)
  hydrogen bonds       : angle       3.69101 ( 2133)
  metal coordination   : bond        0.01347 (    8)
  metal coordination   : angle       6.07265 (    9)
  link_TRANS           : bond        0.00293 (    2)
  link_TRANS           : angle       0.45306 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.8471 (m110) cc_final: 0.8253 (m110)
REVERT: C   75 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7885 (mmtt)
REVERT: D   51 ASP cc_start: 0.8013 (p0) cc_final: 0.7737 (p0)
REVERT: D   71 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7631 (mm-30)
REVERT: F   73 THR cc_start: 0.9448 (t) cc_final: 0.9168 (m)
REVERT: F   74 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7732 (tm-30)
REVERT: H   68 ASP cc_start: 0.9193 (t70) cc_final: 0.8893 (t0)
REVERT: L    7 ASN cc_start: 0.9612 (m-40) cc_final: 0.9351 (m110)
REVERT: L   32 HIS cc_start: 0.7632 (m90) cc_final: 0.7334 (m90)
REVERT: L   63 LYS cc_start: 0.8945 (mttp) cc_final: 0.8638 (mtmm)
REVERT: L   79 ASN cc_start: 0.7312 (m-40) cc_final: 0.6653 (m110)
REVERT: M    1 MET cc_start: 0.8579 (tmm) cc_final: 0.7905 (tmm)
  outliers start: 22
  outliers final: 19
  residues processed: 185
  average time/residue: 0.1438
  time to fit residues: 37.6065
Evaluate side-chains
  184 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 100 optimal weight:    9.9990
   chunk 39 optimal weight:    0.6980
   chunk 101 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    0.1980
   chunk 49 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
E 108 ASN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.140176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.091522 restraints weight = 36884.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.091410 restraints weight = 21549.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.092247 restraints weight = 17937.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.092874 restraints weight = 14454.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.093111 restraints weight = 13540.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15482  Z= 0.155
  Angle     :  0.573   9.319  22186  Z= 0.326
  Chirality :  0.035   0.172   2516
  Planarity :  0.005   0.047   1794
  Dihedral  : 28.852 178.818   4413
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.18 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.26), residues: 1057
  helix:  2.34 (0.21), residues: 648
  sheet:  1.79 (0.76), residues: 53
  loop : -0.99 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  99 
 TYR   0.026   0.001   TYR H  40 
 PHE   0.016   0.001   PHE L  50 
 TRP   0.036   0.003   TRP L 141 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (15472)
  covalent geometry    : angle       0.56443 (22171)
  hydrogen bonds       : bond        0.04448 (  842)
  hydrogen bonds       : angle       3.26946 ( 2133)
  metal coordination   : bond        0.00821 (    8)
  metal coordination   : angle       5.05712 (    9)
  link_TRANS           : bond        0.00063 (    2)
  link_TRANS           : angle       0.37731 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8387 (tpp80) cc_final: 0.7767 (ttm110)
REVERT: B   25 ASN cc_start: 0.8404 (m110) cc_final: 0.8120 (m110)
REVERT: D   40 TYR cc_start: 0.9233 (m-80) cc_final: 0.8462 (m-80)
REVERT: D   51 ASP cc_start: 0.8165 (p0) cc_final: 0.7939 (p0)
REVERT: D   71 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7489 (mm-30)
REVERT: D  116 LYS cc_start: 0.8448 (tppt) cc_final: 0.8193 (ttmm)
REVERT: E   59 GLU cc_start: 0.7941 (pt0) cc_final: 0.7696 (pm20)
REVERT: E   90 MET cc_start: 0.8298 (mmm) cc_final: 0.7992 (mmp)
REVERT: F   73 THR cc_start: 0.9469 (t) cc_final: 0.9200 (m)
REVERT: F   74 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7692 (tm-30)
REVERT: H   68 ASP cc_start: 0.9210 (t70) cc_final: 0.8868 (t0)
REVERT: L    4 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8038 (pttm)
REVERT: L    7 ASN cc_start: 0.9447 (m-40) cc_final: 0.9188 (m110)
REVERT: L   32 HIS cc_start: 0.7820 (m90) cc_final: 0.7570 (m90)
REVERT: M    1 MET cc_start: 0.8055 (tmm) cc_final: 0.7214 (tmm)
  outliers start: 21
  outliers final: 15
  residues processed: 183
  average time/residue: 0.1414
  time to fit residues: 36.5621
Evaluate side-chains
  180 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   66 LYS
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 73 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 102 optimal weight:    0.2980
   chunk 60 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 128 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.140578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.083637 restraints weight = 47953.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.085784 restraints weight = 23525.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.086910 restraints weight = 15151.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.086864 restraints weight = 14234.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.087031 restraints weight = 13402.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15482  Z= 0.153
  Angle     :  0.568   8.608  22186  Z= 0.322
  Chirality :  0.035   0.178   2516
  Planarity :  0.004   0.045   1794
  Dihedral  : 28.877 178.242   4413
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.02 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.26), residues: 1057
  helix:  2.42 (0.21), residues: 650
  sheet:  1.62 (0.78), residues: 48
  loop : -1.03 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.026   0.001   TYR H  40 
 PHE   0.017   0.001   PHE L  50 
 TRP   0.026   0.003   TRP L 141 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (15472)
  covalent geometry    : angle       0.55948 (22171)
  hydrogen bonds       : bond        0.04339 (  842)
  hydrogen bonds       : angle       3.19204 ( 2133)
  metal coordination   : bond        0.00916 (    8)
  metal coordination   : angle       4.89907 (    9)
  link_TRANS           : bond        0.00061 (    2)
  link_TRANS           : angle       0.14943 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7805 (ttm110)
REVERT: B   25 ASN cc_start: 0.8405 (m110) cc_final: 0.8128 (m110)
REVERT: C   74 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8514 (mttm)
REVERT: D   40 TYR cc_start: 0.9223 (m-80) cc_final: 0.8537 (m-80)
REVERT: D   51 ASP cc_start: 0.7964 (p0) cc_final: 0.7727 (p0)
REVERT: F   73 THR cc_start: 0.9516 (t) cc_final: 0.9277 (m)
REVERT: F   74 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7647 (tm-30)
REVERT: G   13 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8311 (mmtt)
REVERT: H   68 ASP cc_start: 0.9144 (t70) cc_final: 0.8841 (t0)
REVERT: K   83 HIS cc_start: 0.7871 (t-90) cc_final: 0.7556 (t-170)
REVERT: L    4 LYS cc_start: 0.8909 (ptpt) cc_final: 0.8379 (pttm)
REVERT: L    7 ASN cc_start: 0.9606 (m-40) cc_final: 0.9311 (m110)
REVERT: L   60 TYR cc_start: 0.8868 (t80) cc_final: 0.8494 (t80)
REVERT: L   74 TYR cc_start: 0.7205 (t80) cc_final: 0.6708 (t80)
REVERT: M    1 MET cc_start: 0.8430 (tmm) cc_final: 0.7554 (tmm)
  outliers start: 24
  outliers final: 19
  residues processed: 192
  average time/residue: 0.1375
  time to fit residues: 37.1944
Evaluate side-chains
  187 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   85 CYS
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 126 optimal weight:    8.9990
   chunk 60 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
L  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.140187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.095642 restraints weight = 40448.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.096305 restraints weight = 33665.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.096524 restraints weight = 33548.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.097306 restraints weight = 19062.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.098885 restraints weight = 16503.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15482  Z= 0.160
  Angle     :  0.571   9.288  22186  Z= 0.323
  Chirality :  0.035   0.183   2516
  Planarity :  0.004   0.044   1794
  Dihedral  : 28.895 178.215   4413
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.99 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.26), residues: 1057
  helix:  2.43 (0.21), residues: 650
  sheet:  1.52 (0.78), residues: 48
  loop : -1.00 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.028   0.002   TYR H  83 
 PHE   0.018   0.001   PHE L  50 
 TRP   0.034   0.004   TRP L  33 
 HIS   0.002   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (15472)
  covalent geometry    : angle       0.56312 (22171)
  hydrogen bonds       : bond        0.04413 (  842)
  hydrogen bonds       : angle       3.17133 ( 2133)
  metal coordination   : bond        0.00950 (    8)
  metal coordination   : angle       4.87645 (    9)
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.15630 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8373 (tpp80) cc_final: 0.7889 (ttm110)
REVERT: B   25 ASN cc_start: 0.8430 (m110) cc_final: 0.8147 (m110)
REVERT: C   74 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8492 (mttm)
REVERT: D   40 TYR cc_start: 0.9251 (m-80) cc_final: 0.8586 (m-80)
REVERT: D   51 ASP cc_start: 0.7999 (p0) cc_final: 0.7777 (p0)
REVERT: D   71 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7572 (mm-30)
REVERT: F   73 THR cc_start: 0.9537 (t) cc_final: 0.9302 (m)
REVERT: F   74 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: H   68 ASP cc_start: 0.9188 (t70) cc_final: 0.8837 (t0)
REVERT: L    4 LYS cc_start: 0.8569 (ptpt) cc_final: 0.7882 (pttm)
REVERT: L   30 MET cc_start: 0.7612 (tpp) cc_final: 0.7376 (tpt)
REVERT: L   38 MET cc_start: 0.8069 (pmm) cc_final: 0.7732 (pmm)
REVERT: L   63 LYS cc_start: 0.9048 (mttp) cc_final: 0.8759 (mttp)
REVERT: M    1 MET cc_start: 0.7835 (tmm) cc_final: 0.7030 (tmm)
  outliers start: 23
  outliers final: 19
  residues processed: 184
  average time/residue: 0.1433
  time to fit residues: 37.3564
Evaluate side-chains
  186 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 122 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 103 optimal weight:    7.9990
   chunk 110 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.140043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.093536 restraints weight = 40501.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.093612 restraints weight = 28025.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.093628 restraints weight = 30518.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.094575 restraints weight = 17528.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.095659 restraints weight = 14990.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15482  Z= 0.168
  Angle     :  0.581   9.309  22186  Z= 0.327
  Chirality :  0.035   0.170   2516
  Planarity :  0.004   0.045   1794
  Dihedral  : 28.932 178.111   4413
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.07 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.26), residues: 1057
  helix:  2.44 (0.21), residues: 650
  sheet:  1.24 (0.73), residues: 53
  loop : -1.01 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.037   0.002   TYR H  83 
 PHE   0.020   0.001   PHE L  50 
 TRP   0.031   0.003   TRP L  33 
 HIS   0.003   0.001   HIS K  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (15472)
  covalent geometry    : angle       0.57230 (22171)
  hydrogen bonds       : bond        0.04570 (  842)
  hydrogen bonds       : angle       3.19785 ( 2133)
  metal coordination   : bond        0.00976 (    8)
  metal coordination   : angle       4.96081 (    9)
  link_TRANS           : bond        0.00062 (    2)
  link_TRANS           : angle       0.14578 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8385 (tpp80) cc_final: 0.7902 (ttm110)
REVERT: B   25 ASN cc_start: 0.8404 (m110) cc_final: 0.8106 (m110)
REVERT: C   74 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8519 (mttm)
REVERT: D   40 TYR cc_start: 0.9274 (m-80) cc_final: 0.8551 (m-80)
REVERT: D   51 ASP cc_start: 0.8048 (p0) cc_final: 0.7830 (p0)
REVERT: D   71 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7609 (mm-30)
REVERT: F   73 THR cc_start: 0.9523 (t) cc_final: 0.9270 (m)
REVERT: F   74 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7614 (tm-30)
REVERT: G   72 ASP cc_start: 0.8445 (m-30) cc_final: 0.8237 (m-30)
REVERT: H   68 ASP cc_start: 0.9251 (t70) cc_final: 0.8941 (t0)
REVERT: K   83 HIS cc_start: 0.7609 (t-90) cc_final: 0.7396 (t-170)
REVERT: L   63 LYS cc_start: 0.9084 (mttp) cc_final: 0.8745 (mttp)
REVERT: L   81 ASN cc_start: 0.8164 (p0) cc_final: 0.7692 (p0)
REVERT: M    1 MET cc_start: 0.7989 (tmm) cc_final: 0.7119 (tmm)
  outliers start: 22
  outliers final: 22
  residues processed: 188
  average time/residue: 0.1417
  time to fit residues: 37.5896
Evaluate side-chains
  192 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
L  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.094637 restraints weight = 42141.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.095023 restraints weight = 30190.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.095192 restraints weight = 29898.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.096019 restraints weight = 17357.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.097301 restraints weight = 14921.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15482  Z= 0.160
  Angle     :  0.581   9.563  22186  Z= 0.326
  Chirality :  0.035   0.173   2516
  Planarity :  0.004   0.044   1794
  Dihedral  : 28.921 178.342   4413
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.61 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.26), residues: 1057
  helix:  2.48 (0.21), residues: 649
  sheet:  1.02 (0.72), residues: 53
  loop : -1.06 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.026   0.001   TYR H  40 
 PHE   0.020   0.001   PHE L  50 
 TRP   0.046   0.004   TRP L  33 
 HIS   0.006   0.001   HIS L  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (15472)
  covalent geometry    : angle       0.57313 (22171)
  hydrogen bonds       : bond        0.04436 (  842)
  hydrogen bonds       : angle       3.16864 ( 2133)
  metal coordination   : bond        0.01048 (    8)
  metal coordination   : angle       4.92674 (    9)
  link_TRANS           : bond        0.00046 (    2)
  link_TRANS           : angle       0.11535 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8391 (tpp80) cc_final: 0.7915 (ttm110)
REVERT: B   25 ASN cc_start: 0.8445 (m110) cc_final: 0.8147 (m110)
REVERT: C   61 GLU cc_start: 0.9211 (tp30) cc_final: 0.8989 (tp30)
REVERT: C   74 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8515 (mttm)
REVERT: D   40 TYR cc_start: 0.9245 (m-80) cc_final: 0.8531 (m-80)
REVERT: D   51 ASP cc_start: 0.8065 (p0) cc_final: 0.7841 (p0)
REVERT: D   71 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7519 (mm-30)
REVERT: F   73 THR cc_start: 0.9527 (t) cc_final: 0.9275 (m)
REVERT: F   74 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: F   88 TYR cc_start: 0.8380 (m-10) cc_final: 0.7964 (m-10)
REVERT: H   68 ASP cc_start: 0.9219 (t70) cc_final: 0.8920 (t0)
REVERT: K   83 HIS cc_start: 0.7928 (t-90) cc_final: 0.7702 (t-170)
REVERT: L   81 ASN cc_start: 0.8041 (p0) cc_final: 0.7442 (p0)
REVERT: M    1 MET cc_start: 0.7958 (tmm) cc_final: 0.7080 (tmm)
  outliers start: 25
  outliers final: 21
  residues processed: 185
  average time/residue: 0.1382
  time to fit residues: 36.2475
Evaluate side-chains
  191 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 120 optimal weight:    8.9990
   chunk 116 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 127 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.138604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.081176 restraints weight = 45625.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.083366 restraints weight = 26963.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.083608 restraints weight = 18199.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.083842 restraints weight = 16188.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.084061 restraints weight = 15699.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  15482  Z= 0.196
  Angle     :  0.612   9.198  22186  Z= 0.340
  Chirality :  0.036   0.169   2516
  Planarity :  0.005   0.047   1794
  Dihedral  : 29.035 177.785   4413
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.37 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.26), residues: 1057
  helix:  2.37 (0.21), residues: 649
  sheet:  0.96 (0.73), residues: 53
  loop : -1.11 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.031   0.002   TYR H  40 
 PHE   0.020   0.002   PHE L  50 
 TRP   0.037   0.003   TRP L  33 
 HIS   0.004   0.001   HIS L  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (15472)
  covalent geometry    : angle       0.60230 (22171)
  hydrogen bonds       : bond        0.04983 (  842)
  hydrogen bonds       : angle       3.30580 ( 2133)
  metal coordination   : bond        0.01116 (    8)
  metal coordination   : angle       5.34598 (    9)
  link_TRANS           : bond        0.00094 (    2)
  link_TRANS           : angle       0.16220 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   61 GLU cc_start: 0.9178 (tp30) cc_final: 0.8704 (tp30)
REVERT: C   74 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8465 (mttm)
REVERT: D   40 TYR cc_start: 0.9288 (m-80) cc_final: 0.8620 (m-80)
REVERT: D   51 ASP cc_start: 0.8035 (p0) cc_final: 0.7815 (p0)
REVERT: D   71 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7577 (mm-30)
REVERT: F   73 THR cc_start: 0.9531 (t) cc_final: 0.9278 (m)
REVERT: F   74 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7566 (tm-30)
REVERT: G   72 ASP cc_start: 0.8508 (m-30) cc_final: 0.8290 (m-30)
REVERT: H   68 ASP cc_start: 0.9191 (t70) cc_final: 0.8912 (t0)
REVERT: K   83 HIS cc_start: 0.7819 (t-90) cc_final: 0.7482 (t-170)
REVERT: L   81 ASN cc_start: 0.8461 (p0) cc_final: 0.8083 (p0)
REVERT: M    1 MET cc_start: 0.8527 (tmm) cc_final: 0.7553 (tmm)
  outliers start: 24
  outliers final: 21
  residues processed: 184
  average time/residue: 0.1434
  time to fit residues: 37.7097
Evaluate side-chains
  190 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    0.5980
   chunk 72 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 87 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
L  46 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.140705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.090702 restraints weight = 35481.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.091288 restraints weight = 21377.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.091820 restraints weight = 17500.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.092276 restraints weight = 14735.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.092574 restraints weight = 13758.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15482  Z= 0.153
  Angle     :  0.585  10.026  22186  Z= 0.327
  Chirality :  0.035   0.161   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 28.934 178.693   4413
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.81 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.26), residues: 1057
  helix:  2.49 (0.21), residues: 649
  sheet:  0.88 (0.73), residues: 53
  loop : -1.10 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.025   0.001   TYR H  40 
 PHE   0.020   0.001   PHE L  50 
 TRP   0.035   0.004   TRP L  33 
 HIS   0.006   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (15472)
  covalent geometry    : angle       0.57740 (22171)
  hydrogen bonds       : bond        0.04373 (  842)
  hydrogen bonds       : angle       3.15908 ( 2133)
  metal coordination   : bond        0.01138 (    8)
  metal coordination   : angle       4.81169 (    9)
  link_TRANS           : bond        0.00040 (    2)
  link_TRANS           : angle       0.09242 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.8172 (m-40) cc_final: 0.7933 (m110)
REVERT: C   61 GLU cc_start: 0.9215 (tp30) cc_final: 0.8723 (tp30)
REVERT: C   74 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8523 (mttm)
REVERT: D   40 TYR cc_start: 0.9230 (m-80) cc_final: 0.8436 (m-80)
REVERT: D   71 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7594 (mm-30)
REVERT: F   73 THR cc_start: 0.9535 (t) cc_final: 0.9261 (m)
REVERT: F   74 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: G   72 ASP cc_start: 0.8402 (m-30) cc_final: 0.8197 (m-30)
REVERT: H   68 ASP cc_start: 0.9165 (t70) cc_final: 0.8893 (t0)
REVERT: K   83 HIS cc_start: 0.7709 (t-90) cc_final: 0.7438 (t-170)
REVERT: L   81 ASN cc_start: 0.8105 (p0) cc_final: 0.7462 (p0)
REVERT: M    1 MET cc_start: 0.7949 (tmm) cc_final: 0.7050 (tmm)
  outliers start: 21
  outliers final: 21
  residues processed: 183
  average time/residue: 0.1256
  time to fit residues: 33.2004
Evaluate side-chains
  187 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   74 TYR
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 111 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   chunk 114 optimal weight:    0.0010
   chunk 42 optimal weight:    0.5980
   chunk 121 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 66 optimal weight:    0.3980
   overall best weight:    0.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.141582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.083519 restraints weight = 48074.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.086314 restraints weight = 25433.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.087838 restraints weight = 16834.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.087903 restraints weight = 13156.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.088150 restraints weight = 13319.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.146
  Angle     :  0.585   9.654  22186  Z= 0.327
  Chirality :  0.035   0.175   2516
  Planarity :  0.004   0.045   1794
  Dihedral  : 28.896 178.606   4413
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.45 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.26), residues: 1057
  helix:  2.51 (0.20), residues: 649
  sheet:  0.75 (0.74), residues: 53
  loop : -1.09 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.042   0.002   TYR F  88 
 PHE   0.020   0.001   PHE L  50 
 TRP   0.033   0.003   TRP L  33 
 HIS   0.005   0.001   HIS L  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (15472)
  covalent geometry    : angle       0.57829 (22171)
  hydrogen bonds       : bond        0.04209 (  842)
  hydrogen bonds       : angle       3.14551 ( 2133)
  metal coordination   : bond        0.01082 (    8)
  metal coordination   : angle       4.52774 (    9)
  link_TRANS           : bond        0.00106 (    2)
  link_TRANS           : angle       0.43411 (    6)

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

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.8165 (m-40) cc_final: 0.7913 (m110)
REVERT: C   61 GLU cc_start: 0.9189 (tp30) cc_final: 0.8697 (tp30)
REVERT: C   74 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8507 (mttm)
REVERT: D   40 TYR cc_start: 0.9238 (m-80) cc_final: 0.8564 (m-80)
REVERT: D   71 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7733 (mm-30)
REVERT: F   73 THR cc_start: 0.9564 (t) cc_final: 0.9234 (m)
REVERT: F   74 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7633 (tm-30)
REVERT: H   68 ASP cc_start: 0.9176 (t70) cc_final: 0.8868 (t0)
REVERT: L   72 ARG cc_start: 0.7289 (ttt180) cc_final: 0.6553 (ttt180)
REVERT: L   81 ASN cc_start: 0.8420 (p0) cc_final: 0.7965 (p0)
REVERT: M    1 MET cc_start: 0.8493 (tmm) cc_final: 0.7521 (tmm)
  outliers start: 21
  outliers final: 18
  residues processed: 182
  average time/residue: 0.1345
  time to fit residues: 35.2688
Evaluate side-chains
  187 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   51 CYS
Chi-restraints excluded: chain L residue   92 GLN
Chi-restraints excluded: chain L residue  103 LEU
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    3 ILE
Chi-restraints excluded: chain M residue   23 ILE
Chi-restraints excluded: chain M residue   67 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 128 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 113 optimal weight:    0.0970
   chunk 24 optimal weight:    0.7980
   chunk 87 optimal weight:    5.9990
   chunk 123 optimal weight:   30.0000
   chunk 127 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.141352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.095243 restraints weight = 41850.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.095276 restraints weight = 28311.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.096289 restraints weight = 20621.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.098847 restraints weight = 14847.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.098708 restraints weight = 12978.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.152
  Angle     :  0.589   9.566  22186  Z= 0.328
  Chirality :  0.035   0.176   2516
  Planarity :  0.005   0.044   1794
  Dihedral  : 28.896 178.454   4413
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 20.35 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.26), residues: 1057
  helix:  2.46 (0.20), residues: 649
  sheet:  0.62 (0.72), residues: 53
  loop : -1.09 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.048   0.002   TYR F  88 
 PHE   0.019   0.001   PHE L  50 
 TRP   0.032   0.004   TRP L  33 
 HIS   0.005   0.001   HIS L  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15472)
  covalent geometry    : angle       0.58165 (22171)
  hydrogen bonds       : bond        0.04290 (  842)
  hydrogen bonds       : angle       3.14777 ( 2133)
  metal coordination   : bond        0.01078 (    8)
  metal coordination   : angle       4.57127 (    9)
  link_TRANS           : bond        0.00049 (    2)
  link_TRANS           : angle       0.47658 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2548.74 seconds
wall clock time: 44 minutes 40.86 seconds (2680.86 seconds total)