Starting phenix.real_space_refine
on Sat May 17 14:59:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jhg_36265/05_2025/8jhg_36265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhg_36265/05_2025/8jhg_36265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jhg_36265/05_2025/8jhg_36265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhg_36265/05_2025/8jhg_36265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhg_36265/05_2025/8jhg_36265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhg_36265/05_2025/8jhg_36265.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1777 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     320      5.49       5
     S      35      5.16       5
     C    8303      2.51       5
     N    2767      2.21       5
     O    3403      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14829
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "K"
      Number of atoms: 2019
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 256, 2014
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 40
      Conformer: "B"
        Number of residues, atoms: 256, 2014
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 40
          bond proxies already assigned to first conformer: 2045
    Chain: "A"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 826
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 97}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 672
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 854
          Classifications: {'peptide': 110}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 693
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 892
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 5, 'TRANS': 109}
    Chain: "H"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 740
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "I"
      Number of atoms: 3253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 3253
          Classifications: {'DNA': 160}
          Link IDs: {'rna3p': 159}
    Chain: "J"
      Number of atoms: 3307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 3307
          Classifications: {'DNA': 160}
          Link IDs: {'rna3p': 159}
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' ZN': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1731  SG  CYS K 319      83.419  30.899  85.584  1.00159.41           S
  ATOM   1746  SG  CYS K 321      84.413  34.101  84.485  1.00163.58           S

  Time building chain proxies: 8.97, per 1000 atoms: 0.60
  Number of scatterers: 14829
  At special positions: 0
  Unit cell: (110.4, 123.28, 141.68, 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      1     29.99
     S      35     16.00
     P     320     15.00
     O    3403      8.00
     N    2767      7.00
     C    8303      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
  Time building additional restraints: 3.29
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 401 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 321 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 319 "


  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1944

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 8 sheets defined
      59.5% alpha, 3.1% beta
      130 base pairs and 279 stacking pairs defined.
    Time for finding SS restraints: 5.85
  Creating SS restraints...
    Processing helix  chain 'K' and resid 77 through 89
    Processing helix  chain 'K' and resid 89 through 94
    Processing helix  chain 'K' and resid 140 through 147
      removed outlier: 3.603A  pdb=" N   PHE K 144 " --> pdb=" O   VAL K 140 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 149 through 159
    Processing helix  chain 'K' and resid 160 through 170
    Processing helix  chain 'K' and resid 171 through 188
    Processing helix  chain 'K' and resid 321 through 327
    Processing helix  chain 'K' and resid 356 through 361
    Processing helix  chain 'A' and resid 46 through 57
      removed outlier: 3.716A  pdb=" N   GLU A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.877A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 113
      removed outlier: 3.994A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TYR A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 116
      No H-bonds generated for 'chain 'A' and resid 114 through 116'
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.605A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.538A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.547A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.701A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU C  51 " --> pdb=" O   ALA C  47 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA C  52 " --> pdb=" O   PRO C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.511A  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 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.709A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.670A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.596A  pdb=" N   HIS D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
      removed outlier: 3.529A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 77
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.761A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.728A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU E 126 " --> pdb=" O   LYS E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.519A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.713A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.705A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY F  94 " --> pdb=" O   LEU F  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.725A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.579A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.594A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 124 through 128
      removed outlier: 3.546A  pdb=" N   LYS G 127 " --> pdb=" O   HIS G 124 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.691A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.704A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU H  99 " --> pdb=" O   VAL H  95 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 115
    Processing helix  chain 'H' and resid 116 through 121
      removed outlier: 4.041A  pdb=" N   SER H 120 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 196 through 199
      removed outlier: 3.590A  pdb=" N   LEU K 198 " --> pdb=" O   LYS K 211 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 231 through 233
      removed outlier: 3.991A  pdb=" N   MET F  20 " --> pdb=" O   VAL K 252 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.702A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
      removed outlier: 3.555A  pdb=" N   THR C 101 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.818A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.646A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.390A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    418 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      338 hydrogen bonds
      676 hydrogen bond angles
      0 basepair planarities
      130 basepair parallelities
      279 stacking parallelities
  Total time for adding SS restraints: 5.55

  Time building geometry restraints manager: 3.96 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3140
        1.33 -     1.45: 4873
        1.45 -     1.57: 7043
        1.57 -     1.69: 638
        1.69 -     1.81: 55
  Bond restraints: 15749
  Sorted by residual:
  bond pdb=" N   LEU K 351 "
       pdb=" CA  LEU K 351 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.039 1.29e-02 6.01e+03 9.31e+00
  bond pdb=" N   THR K 354 "
       pdb=" CA  THR K 354 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.040 1.33e-02 5.65e+03 8.84e+00
  bond pdb=" N   ARG K 352 "
       pdb=" CA  ARG K 352 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 1.33e-02 5.65e+03 8.57e+00
  bond pdb=" C2  SAM K 402 "
       pdb=" N3  SAM K 402 "
    ideal  model  delta    sigma   weight residual
    1.322  1.380 -0.058 2.00e-02 2.50e+03 8.34e+00
  bond pdb=" C8  SAM K 402 "
       pdb=" N7  SAM K 402 "
    ideal  model  delta    sigma   weight residual
    1.298  1.353 -0.055 2.00e-02 2.50e+03 7.48e+00
  ... (remaining 15744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 22151
        1.83 -     3.66: 421
        3.66 -     5.49: 39
        5.49 -     7.32: 8
        7.32 -     9.15: 4
  Bond angle restraints: 22623
  Sorted by residual:
  angle pdb=" CA  ARG K 352 "
        pdb=" C   ARG K 352 "
        pdb=" O   ARG K 352 "
      ideal   model   delta    sigma   weight residual
     121.58  116.35    5.23 1.16e+00 7.43e-01 2.03e+01
  angle pdb=" N   ILE G 111 "
        pdb=" CA  ILE G 111 "
        pdb=" C   ILE G 111 "
      ideal   model   delta    sigma   weight residual
     113.20  109.41    3.79 9.60e-01 1.09e+00 1.56e+01
  angle pdb=" CA  TRP K 218 "
        pdb=" C   TRP K 218 "
        pdb=" O   TRP K 218 "
      ideal   model   delta    sigma   weight residual
     121.33  117.73    3.60 1.08e+00 8.57e-01 1.11e+01
  angle pdb=" C   ARG K 220 "
        pdb=" CA  ARG K 220 "
        pdb=" CB  ARG K 220 "
      ideal   model   delta    sigma   weight residual
     116.54  112.82    3.72 1.15e+00 7.56e-01 1.05e+01
  angle pdb=" N   LYS K 356 "
        pdb=" CA  LYS K 356 "
        pdb=" C   LYS K 356 "
      ideal   model   delta    sigma   weight residual
     113.18  108.92    4.26 1.33e+00 5.65e-01 1.03e+01
  ... (remaining 22618 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.94: 7124
       34.94 -    69.87: 1521
       69.87 -   104.81: 19
      104.81 -   139.74: 1
      139.74 -   174.68: 3
  Dihedral angle restraints: 8668
    sinusoidal: 5654
      harmonic: 3014
  Sorted by residual:
  dihedral pdb=" CA  ARG F  19 "
           pdb=" C   ARG F  19 "
           pdb=" N   MET F  20 "
           pdb=" CA  MET F  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.64  -20.36     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" C4'  DT I  99 "
           pdb=" C3'  DT I  99 "
           pdb=" O3'  DT I  99 "
           pdb=" P    DA I 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   34.68 -174.68     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT J 138 "
           pdb=" C3'  DT J 138 "
           pdb=" O3'  DT J 138 "
           pdb=" P    DC J 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.35  153.65     1      3.50e+01 8.16e-04 1.49e+01
  ... (remaining 8665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1833
       0.032 -    0.064: 547
       0.064 -    0.096: 103
       0.096 -    0.128: 57
       0.128 -    0.160: 8
  Chirality restraints: 2548
  Sorted by residual:
  chirality pdb=" C2' SAM K 402 "
            pdb=" C1' SAM K 402 "
            pdb=" C3' SAM K 402 "
            pdb=" O2' SAM K 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.60   -0.16 2.00e-01 2.50e+01 6.39e-01
  chirality pdb=" CA  LYS B  31 "
            pdb=" N   LYS B  31 "
            pdb=" C   LYS B  31 "
            pdb=" CB  LYS B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" C1'  DA J 161 "
            pdb=" O4'  DA J 161 "
            pdb=" C2'  DA J 161 "
            pdb=" N9   DA J 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.27    0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 2545 not shown)

  Planarity restraints: 1763
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG K 352 "   -0.020 2.00e-02 2.50e+03   4.12e-02 1.70e+01
        pdb=" C   ARG K 352 "    0.071 2.00e-02 2.50e+03
        pdb=" O   ARG K 352 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLU K 353 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU K 198 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.88e+00
        pdb=" N   PRO K 199 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO K 199 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO K 199 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J 161 "    0.021 2.00e-02 2.50e+03   1.33e-02 4.84e+00
        pdb=" N9   DA J 161 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DA J 161 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DA J 161 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DA J 161 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DA J 161 "    0.010 2.00e-02 2.50e+03
        pdb=" N6   DA J 161 "    0.004 2.00e-02 2.50e+03
        pdb=" N1   DA J 161 "   -0.018 2.00e-02 2.50e+03
        pdb=" C2   DA J 161 "    0.015 2.00e-02 2.50e+03
        pdb=" N3   DA J 161 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4   DA J 161 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1760 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 590
        2.70 -     3.25: 13135
        3.25 -     3.80: 25464
        3.80 -     4.35: 31687
        4.35 -     4.90: 46568
  Nonbonded interactions: 117444
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" OG  SER K 255 "
            pdb=" O   LYS K 258 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" O   SER K 193 "
            pdb=" NZ  LYS K 216 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" N2   DG J 159 "
            pdb=" O6   DG J 160 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" N3   DT I   7 "
            pdb=" O2   DT J 162 "
     model   vdw
     2.263 3.120
  ... (remaining 117439 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' and resid 38 through 134)
  selection = (chain 'E' and ((resid 38 through 39 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 40 through 60 or (resid 61 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 62 through 134))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 19 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and (resid 15 through 75 or (resid 76 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 77 through 124))
}
ncs_group {
  reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 75 through 122))
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     40.480
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  15751  Z= 0.181
  Angle     :  0.590   9.152  22623  Z= 0.343
  Chirality :  0.034   0.160   2548
  Planarity :  0.004   0.055   1763
  Dihedral  : 26.864 174.678   6724
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  0.58 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.27), residues: 1019
  helix:  1.78 (0.22), residues: 578
  sheet: -2.95 (0.87), residues: 26
  loop : -2.00 (0.27), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K 218 
 HIS   0.006   0.001   HIS K 245 
 PHE   0.008   0.001   PHE K 281 
 TYR   0.028   0.001   TYR F  88 
 ARG   0.003   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13017 (  756)
  hydrogen bonds       : angle       4.75736 ( 1918)
  metal coordination   : bond        0.00103 (    2)
  covalent geometry    : bond        0.00366 (15749)
  covalent geometry    : angle       0.58978 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 1.101 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7207 (pmm) cc_final: 0.6841 (pmm)
REVERT: K  218 TRP cc_start: 0.5099 (OUTLIER) cc_final: 0.4635 (p90)
REVERT: K  253 MET cc_start: 0.8311 (mtp) cc_final: 0.7931 (mmp)
REVERT: K  294 LEU cc_start: 0.6562 (tp) cc_final: 0.5563 (tp)
REVERT: F   88 TYR cc_start: 0.8973 (m-80) cc_final: 0.8549 (m-80)
  outliers start: 8
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2791
  time to fit residues: 66.5108
Evaluate side-chains
  140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  218 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 100 optimal weight:   30.0000
   chunk 55 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 119 optimal weight:   10.0000
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
K 181 HIS
H  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.111060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.074250 restraints weight = 38038.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.076158 restraints weight = 20341.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.077356 restraints weight = 14311.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15751  Z= 0.171
  Angle     :  0.572   7.623  22623  Z= 0.332
  Chirality :  0.035   0.151   2548
  Planarity :  0.004   0.051   1763
  Dihedral  : 29.357 174.906   4680
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  9.12 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.27), residues: 1019
  helix:  2.17 (0.22), residues: 585
  sheet: -2.82 (0.90), residues: 26
  loop : -2.07 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 218 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE K 183 
 TYR   0.017   0.001   TYR F  88 
 ARG   0.004   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05519 (  756)
  hydrogen bonds       : angle       3.41869 ( 1918)
  metal coordination   : bond        0.00114 (    2)
  covalent geometry    : bond        0.00369 (15749)
  covalent geometry    : angle       0.57212 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 1.121 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7033 (pmm) cc_final: 0.6733 (pmm)
REVERT: K  218 TRP cc_start: 0.4880 (OUTLIER) cc_final: 0.4506 (p90)
REVERT: K  253 MET cc_start: 0.8305 (mtp) cc_final: 0.7835 (mmp)
REVERT: K  294 LEU cc_start: 0.6354 (tp) cc_final: 0.5080 (tp)
REVERT: F   88 TYR cc_start: 0.9020 (m-80) cc_final: 0.8695 (m-80)
REVERT: H   32 GLU cc_start: 0.7881 (pt0) cc_final: 0.7680 (tt0)
  outliers start: 8
  outliers final: 5
  residues processed: 148
  average time/residue: 0.2738
  time to fit residues: 58.3210
Evaluate side-chains
  143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  218 TRP
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain H residue   60 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 17 optimal weight:   20.0000
   chunk 126 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0020
   chunk 123 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    2.7994

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

Flipped N/Q/H residues before XYZ refinement:
F  18 HIS
H  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.110921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.073635 restraints weight = 38172.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.075461 restraints weight = 20606.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.076662 restraints weight = 14594.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15751  Z= 0.172
  Angle     :  0.558   7.262  22623  Z= 0.325
  Chirality :  0.034   0.148   2548
  Planarity :  0.004   0.056   1763
  Dihedral  : 29.275 174.478   4680
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.43 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 1019
  helix:  2.25 (0.21), residues: 587
  sheet: -2.76 (0.93), residues: 26
  loop : -2.02 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K 218 
 HIS   0.003   0.001   HIS D  46 
 PHE   0.009   0.001   PHE K 311 
 TYR   0.016   0.001   TYR F  88 
 ARG   0.005   0.000   ARG K 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05388 (  756)
  hydrogen bonds       : angle       3.25898 ( 1918)
  metal coordination   : bond        0.00128 (    2)
  covalent geometry    : bond        0.00375 (15749)
  covalent geometry    : angle       0.55756 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 1.091 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7033 (pmm) cc_final: 0.6746 (pmm)
REVERT: K  218 TRP cc_start: 0.4986 (OUTLIER) cc_final: 0.4649 (p90)
REVERT: K  253 MET cc_start: 0.8338 (mtp) cc_final: 0.7848 (mmp)
REVERT: K  294 LEU cc_start: 0.6372 (tp) cc_final: 0.5178 (tp)
REVERT: A  113 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7706 (m170)
REVERT: F   88 TYR cc_start: 0.9008 (m-10) cc_final: 0.8729 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 150
  average time/residue: 0.2671
  time to fit residues: 58.0227
Evaluate side-chains
  142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  158 THR
Chi-restraints excluded: chain K residue  218 TRP
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue  108 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 35 optimal weight:    0.0020
   chunk 70 optimal weight:    0.0980
   chunk 104 optimal weight:   10.0000
   chunk 118 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 115 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 80 optimal weight:    9.9990
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
H  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.113645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.077536 restraints weight = 38348.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.079415 restraints weight = 19955.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.080659 restraints weight = 13940.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15751  Z= 0.139
  Angle     :  0.530   9.300  22623  Z= 0.310
  Chirality :  0.033   0.156   2548
  Planarity :  0.004   0.056   1763
  Dihedral  : 29.093 175.416   4680
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.47 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.27), residues: 1019
  helix:  2.61 (0.21), residues: 580
  sheet: -2.68 (0.93), residues: 26
  loop : -1.93 (0.27), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 218 
 HIS   0.003   0.000   HIS B  75 
 PHE   0.006   0.001   PHE D  67 
 TYR   0.014   0.001   TYR F  88 
 ARG   0.004   0.000   ARG D  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03928 (  756)
  hydrogen bonds       : angle       2.94413 ( 1918)
  metal coordination   : bond        0.00043 (    2)
  covalent geometry    : bond        0.00292 (15749)
  covalent geometry    : angle       0.52972 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 1.081 
Fit side-chains
REVERT: K  100 MET cc_start: 0.6961 (pmm) cc_final: 0.6582 (pmm)
REVERT: K  218 TRP cc_start: 0.4935 (OUTLIER) cc_final: 0.4645 (p90)
REVERT: K  253 MET cc_start: 0.8217 (mtp) cc_final: 0.7921 (mmp)
REVERT: K  294 LEU cc_start: 0.6372 (tp) cc_final: 0.5158 (tp)
REVERT: A  113 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7781 (m170)
REVERT: D   97 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8866 (mp)
REVERT: F   88 TYR cc_start: 0.8918 (m-10) cc_final: 0.8245 (m-80)
REVERT: H   46 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6932 (m-70)
  outliers start: 13
  outliers final: 5
  residues processed: 166
  average time/residue: 0.2599
  time to fit residues: 62.9318
Evaluate side-chains
  149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain K residue  218 TRP
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue   46 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 115 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 80 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 66 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 114 optimal weight:   10.0000
   chunk 128 optimal weight:   10.0000
   overall best weight:    3.1386

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.110730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.073899 restraints weight = 38345.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.075656 restraints weight = 20652.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.076813 restraints weight = 14651.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15751  Z= 0.179
  Angle     :  0.561   8.129  22623  Z= 0.325
  Chirality :  0.034   0.150   2548
  Planarity :  0.004   0.058   1763
  Dihedral  : 29.195 174.478   4680
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.09 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.27), residues: 1019
  helix:  2.42 (0.22), residues: 589
  sheet: -2.65 (0.92), residues: 26
  loop : -2.01 (0.27), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 218 
 HIS   0.014   0.001   HIS H  46 
 PHE   0.008   0.001   PHE A 104 
 TYR   0.021   0.001   TYR C  57 
 ARG   0.003   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05412 (  756)
  hydrogen bonds       : angle       3.14902 ( 1918)
  metal coordination   : bond        0.00128 (    2)
  covalent geometry    : bond        0.00396 (15749)
  covalent geometry    : angle       0.56111 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.093 
Fit side-chains
REVERT: K  218 TRP cc_start: 0.5030 (OUTLIER) cc_final: 0.4809 (p90)
REVERT: K  253 MET cc_start: 0.8310 (mtp) cc_final: 0.7741 (mmm)
REVERT: K  294 LEU cc_start: 0.6483 (tp) cc_final: 0.5229 (tp)
REVERT: A  113 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7776 (m170)
REVERT: D   68 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7736 (tp30)
REVERT: D   97 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8861 (mp)
REVERT: F   88 TYR cc_start: 0.8911 (m-10) cc_final: 0.8674 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 150
  average time/residue: 0.2690
  time to fit residues: 58.6541
Evaluate side-chains
  150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain K residue  218 TRP
Chi-restraints excluded: chain K residue  260 CYS
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain G residue   43 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 116 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 128 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 109 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.109931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.072709 restraints weight = 38063.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.074489 restraints weight = 20788.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.075664 restraints weight = 14860.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15751  Z= 0.192
  Angle     :  0.576   8.469  22623  Z= 0.334
  Chirality :  0.035   0.152   2548
  Planarity :  0.004   0.059   1763
  Dihedral  : 29.261 174.515   4680
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.01 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.27), residues: 1019
  helix:  2.32 (0.22), residues: 587
  sheet: -2.69 (0.93), residues: 26
  loop : -2.07 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 218 
 HIS   0.005   0.001   HIS D  46 
 PHE   0.009   0.001   PHE A 104 
 TYR   0.013   0.001   TYR H  80 
 ARG   0.003   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05744 (  756)
  hydrogen bonds       : angle       3.21940 ( 1918)
  metal coordination   : bond        0.00162 (    2)
  covalent geometry    : bond        0.00428 (15749)
  covalent geometry    : angle       0.57649 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 1.097 
Fit side-chains
REVERT: K  218 TRP cc_start: 0.5153 (OUTLIER) cc_final: 0.4891 (p90)
REVERT: K  253 MET cc_start: 0.8230 (mtp) cc_final: 0.7802 (mmp)
REVERT: K  294 LEU cc_start: 0.6432 (tp) cc_final: 0.5040 (tp)
REVERT: A  113 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7809 (m170)
REVERT: D   97 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8874 (mp)
REVERT: H   34 TYR cc_start: 0.8673 (m-80) cc_final: 0.8442 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 149
  average time/residue: 0.2710
  time to fit residues: 58.9196
Evaluate side-chains
  147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  185 TYR
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain K residue  218 TRP
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain H residue  108 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 125 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 100 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 126 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 117 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   overall best weight:    5.7790

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.107642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.070321 restraints weight = 38585.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.072074 restraints weight = 21083.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.073222 restraints weight = 15073.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  15751  Z= 0.262
  Angle     :  0.644   9.249  22623  Z= 0.369
  Chirality :  0.038   0.161   2548
  Planarity :  0.005   0.061   1763
  Dihedral  : 29.525 174.778   4680
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.70 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.26), residues: 1019
  helix:  2.01 (0.21), residues: 585
  sheet: -2.64 (0.94), residues: 26
  loop : -2.24 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 264 
 HIS   0.006   0.001   HIS D  46 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.019   0.002   TYR H  80 
 ARG   0.008   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07058 (  756)
  hydrogen bonds       : angle       3.51125 ( 1918)
  metal coordination   : bond        0.00292 (    2)
  covalent geometry    : bond        0.00600 (15749)
  covalent geometry    : angle       0.64381 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 1.149 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7126 (pmm) cc_final: 0.6666 (pmm)
REVERT: A  113 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7936 (m170)
REVERT: D   97 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8972 (mp)
REVERT: H   34 TYR cc_start: 0.8748 (m-80) cc_final: 0.8526 (m-80)
REVERT: H   59 MET cc_start: 0.9042 (mmm) cc_final: 0.8837 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 152
  average time/residue: 0.2774
  time to fit residues: 60.8368
Evaluate side-chains
  146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  185 TYR
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue  108 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 129 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 93 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
C  89 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.110436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.073427 restraints weight = 38381.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.075288 restraints weight = 20739.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.076489 restraints weight = 14670.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15751  Z= 0.164
  Angle     :  0.581   8.766  22623  Z= 0.335
  Chirality :  0.034   0.155   2548
  Planarity :  0.004   0.057   1763
  Dihedral  : 29.262 174.957   4678
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.86 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 1019
  helix:  2.32 (0.22), residues: 585
  sheet: -2.52 (0.95), residues: 26
  loop : -2.16 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K 218 
 HIS   0.003   0.001   HIS D  46 
 PHE   0.009   0.001   PHE K 281 
 TYR   0.027   0.001   TYR F  88 
 ARG   0.004   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05090 (  756)
  hydrogen bonds       : angle       3.18166 ( 1918)
  metal coordination   : bond        0.00101 (    2)
  covalent geometry    : bond        0.00358 (15749)
  covalent geometry    : angle       0.58146 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.317 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7174 (pmm) cc_final: 0.6730 (pmm)
REVERT: K  253 MET cc_start: 0.7986 (mtp) cc_final: 0.7654 (mmp)
REVERT: K  307 TYR cc_start: 0.6908 (m-80) cc_final: 0.6360 (m-80)
REVERT: A  113 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7759 (m170)
REVERT: H   34 TYR cc_start: 0.8642 (m-80) cc_final: 0.8413 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 150
  average time/residue: 0.2718
  time to fit residues: 60.2780
Evaluate side-chains
  149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   72 MET
Chi-restraints excluded: chain K residue  185 TYR
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain H residue  108 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 123 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 120 optimal weight:   10.0000
   chunk 59 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
G 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.109775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.072712 restraints weight = 38297.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.074527 restraints weight = 21014.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.075676 restraints weight = 14970.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15751  Z= 0.178
  Angle     :  0.591  10.189  22623  Z= 0.339
  Chirality :  0.034   0.151   2548
  Planarity :  0.004   0.057   1763
  Dihedral  : 29.262 174.737   4678
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.51 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 1019
  helix:  2.29 (0.22), residues: 589
  sheet: -2.38 (0.96), residues: 26
  loop : -2.17 (0.27), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP K 218 
 HIS   0.005   0.001   HIS H 106 
 PHE   0.008   0.001   PHE K 311 
 TYR   0.033   0.002   TYR H  80 
 ARG   0.003   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05410 (  756)
  hydrogen bonds       : angle       3.20542 ( 1918)
  metal coordination   : bond        0.00143 (    2)
  covalent geometry    : bond        0.00395 (15749)
  covalent geometry    : angle       0.59080 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.075 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7136 (pmm) cc_final: 0.6681 (pmm)
REVERT: K  237 ILE cc_start: 0.6457 (mm) cc_final: 0.6230 (pt)
REVERT: K  253 MET cc_start: 0.8008 (mtp) cc_final: 0.7562 (mmp)
REVERT: A  113 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7832 (m170)
REVERT: H   34 TYR cc_start: 0.8650 (m-80) cc_final: 0.8438 (m-80)
  outliers start: 15
  outliers final: 12
  residues processed: 142
  average time/residue: 0.2661
  time to fit residues: 54.6319
Evaluate side-chains
  141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  185 TYR
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue   60 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 105 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 101 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.108832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.071838 restraints weight = 38663.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.073690 restraints weight = 20361.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.074850 restraints weight = 14288.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15751  Z= 0.200
  Angle     :  0.601  10.397  22623  Z= 0.345
  Chirality :  0.035   0.154   2548
  Planarity :  0.004   0.057   1763
  Dihedral  : 29.285 174.577   4678
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.51 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 1019
  helix:  2.25 (0.21), residues: 587
  sheet: -2.37 (0.98), residues: 26
  loop : -2.24 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP K 218 
 HIS   0.004   0.001   HIS H 106 
 PHE   0.010   0.001   PHE K 311 
 TYR   0.023   0.002   TYR F  88 
 ARG   0.003   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05819 (  756)
  hydrogen bonds       : angle       3.26472 ( 1918)
  metal coordination   : bond        0.00177 (    2)
  covalent geometry    : bond        0.00450 (15749)
  covalent geometry    : angle       0.60057 (22623)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.101 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7167 (pmm) cc_final: 0.6713 (pmm)
REVERT: K  237 ILE cc_start: 0.6533 (mm) cc_final: 0.6285 (pt)
REVERT: K  253 MET cc_start: 0.8019 (mtp) cc_final: 0.7590 (mmp)
REVERT: A  113 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7814 (m170)
REVERT: H   34 TYR cc_start: 0.8720 (m-80) cc_final: 0.8492 (m-80)
  outliers start: 14
  outliers final: 12
  residues processed: 141
  average time/residue: 0.2746
  time to fit residues: 55.7582
Evaluate side-chains
  141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  185 TYR
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain K residue  265 LEU
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue   60 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 131 optimal weight:   30.0000
   chunk 106 optimal weight:   10.0000
   chunk 45 optimal weight:    0.2980
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   chunk 130 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   overall best weight:    1.4762

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.111539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.075236 restraints weight = 38589.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.077099 restraints weight = 20329.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.078327 restraints weight = 14264.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15751  Z= 0.149
  Angle     :  0.565   9.913  22623  Z= 0.326
  Chirality :  0.033   0.146   2548
  Planarity :  0.004   0.055   1763
  Dihedral  : 29.121 175.253   4678
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 16.86 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.27), residues: 1019
  helix:  2.51 (0.22), residues: 587
  sheet: -2.38 (1.00), residues: 26
  loop : -2.14 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K 218 
 HIS   0.004   0.001   HIS F  18 
 PHE   0.007   0.001   PHE K 281 
 TYR   0.014   0.001   TYR F  88 
 ARG   0.002   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04394 (  756)
  hydrogen bonds       : angle       3.02045 ( 1918)
  metal coordination   : bond        0.00068 (    2)
  covalent geometry    : bond        0.00320 (15749)
  covalent geometry    : angle       0.56459 (22623)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5202.87 seconds
wall clock time: 90 minutes 55.77 seconds (5455.77 seconds total)