Starting phenix.real_space_refine
on Sat Jun 14 05:38:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jhg_36265/06_2025/8jhg_36265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhg_36265/06_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_36265/06_2025/8jhg_36265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhg_36265/06_2025/8jhg_36265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhg_36265/06_2025/8jhg_36265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhg_36265/06_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.93, 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: 3.30
  Conformation dependent library (CDL) restraints added in 1.3 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: 6.49
  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: 6.00

  Time building geometry restraints manager: 3.99 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.170
  Process input model:                     42.270
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.090
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.420
-------------------------------------------------------------------------------
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  : 1.071 
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: 0.2799
  time to fit residues: 66.6722
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  : 1.080 
-------------------------------------------------------------------------------
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 = 0.3804 r_free = 0.3804 target = 0.110878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.074222 restraints weight = 38163.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.076036 restraints weight = 20463.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.077149 restraints weight = 14431.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    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 = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
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  : 1.045 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7039 (pmm) cc_final: 0.6737 (pmm)
REVERT: K  218 TRP cc_start: 0.4884 (OUTLIER) cc_final: 0.4509 (p90)
REVERT: K  253 MET cc_start: 0.8307 (mtp) cc_final: 0.7829 (mmp)
REVERT: K  294 LEU cc_start: 0.6357 (tp) cc_final: 0.5082 (tp)
REVERT: F   88 TYR cc_start: 0.9019 (m-80) cc_final: 0.8698 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 148
  average time/residue: 0.2835
  time to fit residues: 60.3537
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  : 1.157 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 17 optimal weight:   20.0000
   chunk 126 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 98 optimal weight:    0.6980
   chunk 123 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.111743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.074867 restraints weight = 38354.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.076671 restraints weight = 20737.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.077887 restraints weight = 14733.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    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 = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1375

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= 0.156
  Angle     :  0.545   7.105  22623  Z= 0.319
  Chirality :  0.034   0.160   2548
  Planarity :  0.004   0.056   1763
  Dihedral  : 29.215 174.656   4680
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.09 %
    Favored  : 87.64 %
  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:  0.89 (0.27), residues: 1019
  helix:  2.35 (0.21), residues: 587
  sheet: -2.74 (0.93), residues: 26
  loop : -1.99 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 218 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.008   0.001   PHE K 311 
 TYR   0.016   0.001   TYR F  88 
 ARG   0.004   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04921 (  756)
  hydrogen bonds       : angle       3.17374 ( 1918)
  metal coordination   : bond        0.00098 (    2)
  covalent geometry    : bond        0.00336 (15749)
  covalent geometry    : angle       0.54463 (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
  157 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 1.115 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7011 (pmm) cc_final: 0.6724 (pmm)
REVERT: K  218 TRP cc_start: 0.4987 (OUTLIER) cc_final: 0.4647 (p90)
REVERT: K  253 MET cc_start: 0.8290 (mtp) cc_final: 0.7886 (mmp)
REVERT: K  294 LEU cc_start: 0.6358 (tp) cc_final: 0.5136 (tp)
REVERT: A  113 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7687 (m170)
REVERT: F   88 TYR cc_start: 0.8995 (m-80) cc_final: 0.8669 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 151
  average time/residue: 0.2739
  time to fit residues: 60.0353
Evaluate side-chains
  143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
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   45 THR
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain C residue   99 ARG
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:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 104 optimal weight:   10.0000
   chunk 118 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 115 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0270
   chunk 68 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    3.4046

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.109885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.072706 restraints weight = 37985.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.074551 restraints weight = 20400.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.075740 restraints weight = 14420.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    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 = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1566

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= 0.187
  Angle     :  0.572   8.867  22623  Z= 0.332
  Chirality :  0.035   0.161   2548
  Planarity :  0.004   0.058   1763
  Dihedral  : 29.300 174.585   4680
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.05 %
    Favored  : 85.22 %
  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:  2.23 (0.21), residues: 588
  sheet: -2.70 (0.92), residues: 26
  loop : -2.03 (0.27), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 218 
 HIS   0.004   0.001   HIS D  46 
 PHE   0.009   0.001   PHE A 104 
 TYR   0.012   0.001   TYR F  88 
 ARG   0.004   0.000   ARG D  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05834 (  756)
  hydrogen bonds       : angle       3.29052 ( 1918)
  metal coordination   : bond        0.00151 (    2)
  covalent geometry    : bond        0.00414 (15749)
  covalent geometry    : angle       0.57206 (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
  155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 1.233 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7039 (pmm) cc_final: 0.6581 (pmm)
REVERT: K  218 TRP cc_start: 0.5083 (OUTLIER) cc_final: 0.4821 (p90)
REVERT: K  253 MET cc_start: 0.8277 (mtp) cc_final: 0.7808 (mmp)
REVERT: K  282 VAL cc_start: 0.8703 (t) cc_final: 0.8475 (m)
REVERT: K  294 LEU cc_start: 0.6393 (tp) cc_final: 0.5238 (tp)
REVERT: A  113 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.7781 (m170)
REVERT: D   97 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9001 (mp)
  outliers start: 15
  outliers final: 7
  residues processed: 150
  average time/residue: 0.2717
  time to fit residues: 59.9733
Evaluate side-chains
  145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
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 C residue   99 ARG
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain H residue  108 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 3 optimal weight:    7.9990
   chunk 115 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 114 optimal weight:   10.0000
   chunk 128 optimal weight:   10.0000
   overall best weight:    2.3584

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.111379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.074767 restraints weight = 38244.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.076539 restraints weight = 20518.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.077717 restraints weight = 14500.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    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 = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1652

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= 0.161
  Angle     :  0.553   8.251  22623  Z= 0.322
  Chirality :  0.034   0.152   2548
  Planarity :  0.004   0.057   1763
  Dihedral  : 29.209 174.915   4680
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.39 %
    Favored  : 84.64 %
  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:  0.92 (0.27), residues: 1019
  helix:  2.41 (0.22), residues: 587
  sheet: -2.72 (0.91), residues: 26
  loop : -2.03 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 218 
 HIS   0.003   0.001   HIS D  46 
 PHE   0.007   0.001   PHE K 311 
 TYR   0.025   0.001   TYR F  88 
 ARG   0.004   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04941 (  756)
  hydrogen bonds       : angle       3.09823 ( 1918)
  metal coordination   : bond        0.00097 (    2)
  covalent geometry    : bond        0.00350 (15749)
  covalent geometry    : angle       0.55313 (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
  161 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 1.175 
Fit side-chains
REVERT: K  218 TRP cc_start: 0.4997 (OUTLIER) cc_final: 0.4754 (p90)
REVERT: K  253 MET cc_start: 0.8340 (mtp) cc_final: 0.7809 (mmt)
REVERT: K  282 VAL cc_start: 0.8617 (t) cc_final: 0.8384 (m)
REVERT: K  294 LEU cc_start: 0.6401 (tp) cc_final: 0.5139 (tp)
REVERT: A  113 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7744 (m170)
  outliers start: 17
  outliers final: 12
  residues processed: 156
  average time/residue: 0.2654
  time to fit residues: 60.9414
Evaluate side-chains
  147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
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  116 THR
Chi-restraints excluded: chain E residue  112 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 116 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 128 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 109 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0980
   overall best weight:    2.8188

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.110541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.073616 restraints weight = 38061.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.075495 restraints weight = 19933.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.076705 restraints weight = 13945.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
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: 0.8221
moved from start:          0.1783

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= 0.172
  Angle     :  0.563   8.753  22623  Z= 0.326
  Chirality :  0.034   0.148   2548
  Planarity :  0.004   0.058   1763
  Dihedral  : 29.231 174.744   4680
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.74 %
    Favored  : 84.06 %
  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:  0.87 (0.27), residues: 1019
  helix:  2.36 (0.22), residues: 589
  sheet: -2.69 (0.91), residues: 26
  loop : -2.08 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 218 
 HIS   0.003   0.001   HIS D  46 
 PHE   0.007   0.001   PHE A 104 
 TYR   0.011   0.001   TYR C  57 
 ARG   0.004   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05322 (  756)
  hydrogen bonds       : angle       3.12921 ( 1918)
  metal coordination   : bond        0.00131 (    2)
  covalent geometry    : bond        0.00379 (15749)
  covalent geometry    : angle       0.56303 (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
  155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 1.097 
Fit side-chains
REVERT: K  218 TRP cc_start: 0.5086 (OUTLIER) cc_final: 0.4821 (p90)
REVERT: K  253 MET cc_start: 0.8291 (mtp) cc_final: 0.7799 (mmp)
REVERT: K  294 LEU cc_start: 0.6414 (tp) cc_final: 0.5196 (tp)
REVERT: A  113 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7754 (m170)
REVERT: F   88 TYR cc_start: 0.8964 (m-80) cc_final: 0.8630 (m-80)
  outliers start: 19
  outliers final: 16
  residues processed: 148
  average time/residue: 0.2616
  time to fit residues: 56.8349
Evaluate side-chains
  151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
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  260 CYS
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 D residue  116 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  117 VAL
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:    2.9990
   chunk 9 optimal weight:   10.0000
   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:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 117 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   overall best weight:    5.5992

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.107813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.070353 restraints weight = 38570.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.072046 restraints weight = 21438.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.073123 restraints weight = 15298.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    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 = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  15751  Z= 0.258
  Angle     :  0.644   9.220  22623  Z= 0.369
  Chirality :  0.038   0.159   2548
  Planarity :  0.005   0.061   1763
  Dihedral  : 29.479 174.582   4680
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.01 %
    Favored  : 82.79 %
  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:  0.40 (0.26), residues: 1019
  helix:  1.99 (0.21), residues: 586
  sheet: -3.06 (0.92), residues: 24
  loop : -2.25 (0.27), residues: 409

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   0.012   0.001   PHE A 104 
 TYR   0.017   0.002   TYR F  88 
 ARG   0.005   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07096 (  756)
  hydrogen bonds       : angle       3.52896 ( 1918)
  metal coordination   : bond        0.00298 (    2)
  covalent geometry    : bond        0.00590 (15749)
  covalent geometry    : angle       0.64399 (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: 19
    poor density    : 137
  time to evaluate  : 1.072 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7127 (pmm) cc_final: 0.6640 (pmm)
REVERT: K  253 MET cc_start: 0.8219 (mtp) cc_final: 0.7701 (mmp)
REVERT: K  294 LEU cc_start: 0.6607 (tp) cc_final: 0.6385 (tp)
REVERT: K  307 TYR cc_start: 0.7187 (m-80) cc_final: 0.6596 (m-80)
REVERT: A  113 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7908 (m170)
REVERT: H   46 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7447 (m-70)
  outliers start: 19
  outliers final: 13
  residues processed: 151
  average time/residue: 0.2742
  time to fit residues: 60.1122
Evaluate side-chains
  148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
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  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   46 HIS
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:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9980
   chunk 16 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.111655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.075203 restraints weight = 38379.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.077183 restraints weight = 19966.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.078433 restraints weight = 13808.168|
|-----------------------------------------------------------------------------|
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: 0.8182
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15751  Z= 0.150
  Angle     :  0.574   9.970  22623  Z= 0.331
  Chirality :  0.033   0.154   2548
  Planarity :  0.004   0.057   1763
  Dihedral  : 29.158 175.211   4678
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.17 %
    Favored  : 82.45 %
  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:  0.92 (0.27), residues: 1019
  helix:  2.43 (0.22), residues: 585
  sheet: -2.51 (0.95), residues: 26
  loop : -2.07 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP K 218 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE K 281 
 TYR   0.018   0.001   TYR C  57 
 ARG   0.003   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04402 (  756)
  hydrogen bonds       : angle       3.04760 ( 1918)
  metal coordination   : bond        0.00057 (    2)
  covalent geometry    : bond        0.00322 (15749)
  covalent geometry    : angle       0.57374 (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
  156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 1.244 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7134 (pmm) cc_final: 0.6641 (pmm)
REVERT: K  253 MET cc_start: 0.8195 (mtp) cc_final: 0.7804 (mmt)
REVERT: A  113 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7697 (m170)
  outliers start: 12
  outliers final: 7
  residues processed: 151
  average time/residue: 0.2848
  time to fit residues: 62.8433
Evaluate side-chains
  141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  185 TYR
Chi-restraints excluded: chain K residue  203 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 E residue  112 ILE
Chi-restraints excluded: chain G residue   43 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 25 optimal weight:    0.0040
   chunk 39 optimal weight:    0.9980
   chunk 130 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 123 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 59 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    0.9596

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
E  39 HIS
G  68 ASN
G 112 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.112896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.077086 restraints weight = 38522.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.078929 restraints weight = 20499.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.080139 restraints weight = 14375.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    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 = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2259

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= 0.142
  Angle     :  0.559  10.196  22623  Z= 0.321
  Chirality :  0.032   0.145   2548
  Planarity :  0.004   0.056   1763
  Dihedral  : 29.045 175.342   4678
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 17.21 %
    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:  1.12 (0.27), residues: 1019
  helix:  2.58 (0.22), residues: 589
  sheet: -2.41 (0.97), residues: 26
  loop : -2.01 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 264 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.009   0.001   PHE K 281 
 TYR   0.016   0.001   TYR C  57 
 ARG   0.004   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  756)
  hydrogen bonds       : angle       2.93616 ( 1918)
  metal coordination   : bond        0.00048 (    2)
  covalent geometry    : bond        0.00302 (15749)
  covalent geometry    : angle       0.55949 (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
  160 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 1.164 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7139 (pmm) cc_final: 0.6597 (pmm)
REVERT: K  150 LEU cc_start: 0.8393 (mt) cc_final: 0.8056 (pp)
REVERT: K  173 MET cc_start: 0.8134 (tpp) cc_final: 0.7847 (tpp)
REVERT: K  253 MET cc_start: 0.8227 (mtp) cc_final: 0.7923 (mmp)
REVERT: D  117 LYS cc_start: 0.8826 (tptt) cc_final: 0.8182 (tttt)
  outliers start: 9
  outliers final: 6
  residues processed: 155
  average time/residue: 0.2752
  time to fit residues: 62.0199
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  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   72 MET
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain G residue   43 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    0.3980
   chunk 95 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 105 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 97 optimal weight:    0.0770
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.6944

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

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.109891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.072867 restraints weight = 39620.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.074804 restraints weight = 20774.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.076047 restraints weight = 14512.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    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 = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15751  Z= 0.170
  Angle     :  0.577  10.965  22623  Z= 0.331
  Chirality :  0.034   0.148   2548
  Planarity :  0.004   0.061   1763
  Dihedral  : 29.091 174.268   4678
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 17.67 %
    Favored  : 81.29 %
  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:  0.95 (0.27), residues: 1019
  helix:  2.42 (0.22), residues: 590
  sheet: -2.25 (0.99), residues: 26
  loop : -2.07 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 218 
 HIS   0.004   0.001   HIS D  46 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.024   0.001   TYR F  88 
 ARG   0.003   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05108 (  756)
  hydrogen bonds       : angle       3.08552 ( 1918)
  metal coordination   : bond        0.00129 (    2)
  covalent geometry    : bond        0.00376 (15749)
  covalent geometry    : angle       0.57708 (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
  147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 138
  time to evaluate  : 1.034 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7159 (pmm) cc_final: 0.6636 (pmm)
REVERT: K  237 ILE cc_start: 0.6757 (pt) cc_final: 0.6528 (mm)
REVERT: K  253 MET cc_start: 0.8263 (mtp) cc_final: 0.7941 (mmp)
  outliers start: 9
  outliers final: 6
  residues processed: 143
  average time/residue: 0.2563
  time to fit residues: 53.7651
Evaluate side-chains
  140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 134
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  203 TYR
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
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:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 131 optimal weight:   30.0000
   chunk 106 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0060
   chunk 71 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0170
   chunk 130 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0030
   overall best weight:    0.3846

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.113010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.076750 restraints weight = 39693.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.078748 restraints weight = 20555.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.080043 restraints weight = 14233.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    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 = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15751  Z= 0.140
  Angle     :  0.551  10.890  22623  Z= 0.317
  Chirality :  0.032   0.142   2548
  Planarity :  0.004   0.059   1763
  Dihedral  : 28.940 175.284   4678
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 17.67 %
    Favored  : 81.64 %
  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:  1.15 (0.27), residues: 1019
  helix:  2.56 (0.22), residues: 590
  sheet: -2.21 (0.99), residues: 26
  loop : -1.96 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 218 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.006   0.001   PHE D  67 
 TYR   0.015   0.001   TYR C  57 
 ARG   0.005   0.000   ARG K 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  756)
  hydrogen bonds       : angle       2.89059 ( 1918)
  metal coordination   : bond        0.00031 (    2)
  covalent geometry    : bond        0.00298 (15749)
  covalent geometry    : angle       0.55129 (22623)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5406.13 seconds
wall clock time: 93 minutes 32.56 seconds (5612.56 seconds total)