Starting phenix.real_space_refine
on Wed Feb  4 19:29:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t3w_41015/02_2026/8t3w_41015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t3w_41015/02_2026/8t3w_41015.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t3w_41015/02_2026/8t3w_41015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t3w_41015/02_2026/8t3w_41015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t3w_41015/02_2026/8t3w_41015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t3w_41015/02_2026/8t3w_41015.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P     292      5.49       5
     S      32      5.16       5
     C    7249      2.51       5
     N    2425      2.21       5
     O    2999      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13001
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 800
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 543
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "L"
      Number of atoms: 543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 543
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "L"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12166  SG  CYS K 663      94.558  74.806  62.875  1.00139.73           S
  ATOM  12325  SG  CYS K 683      92.501  76.362  60.038  1.00119.37           S
  ATOM  12345  SG  CYS K 686      95.897  74.876  59.264  1.00125.56           S
  ATOM  12049  SG  CYS K 648      85.019  82.149  65.675  1.00162.60           S
  ATOM  12069  SG  CYS K 651      82.233  84.334  67.247  1.00163.36           S
  ATOM  12204  SG  CYS K 668      82.584  80.711  68.198  1.00143.24           S
  ATOM  12227  SG  CYS K 671      81.166  81.285  65.164  1.00136.31           S
  ATOM  12709  SG  CYS L 663      95.523  72.650  83.157  1.00172.78           S
  ATOM  12868  SG  CYS L 683      97.601  72.700  86.835  1.00186.18           S
  ATOM  12888  SG  CYS L 686      94.510  71.743  87.275  1.00190.44           S
  ATOM  12592  SG  CYS L 648     102.961  83.940  81.389  1.00189.02           S
  ATOM  12612  SG  CYS L 651     105.730  86.538  80.694  1.00190.09           S
  ATOM  12747  SG  CYS L 668     105.574  83.267  78.829  1.00189.67           S
  ATOM  12770  SG  CYS L 671     106.608  83.208  82.415  1.00190.98           S

  Time building chain proxies: 2.51, per 1000 atoms: 0.19
  Number of scatterers: 13001
  At special positions: 0
  Unit cell: (127.395, 117.99, 117.99, 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      4     29.99
     S      32     16.00
     P     292     15.00
     O    2999      8.00
     N    2425      7.00
     C    7249      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: 0.98
  Conformation dependent library (CDL) restraints added in 381.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 801 "
        pdb="ZN    ZN K 801 " - pdb=" ND1 HIS K 665 "
        pdb="ZN    ZN K 801 " - pdb=" SG  CYS K 683 "
        pdb="ZN    ZN K 801 " - pdb=" SG  CYS K 663 "
        pdb="ZN    ZN K 801 " - pdb=" SG  CYS K 686 "
      pdb="  ZN K 802 "
        pdb="ZN    ZN K 802 " - pdb=" SG  CYS K 668 "
        pdb="ZN    ZN K 802 " - pdb=" SG  CYS K 651 "
        pdb="ZN    ZN K 802 " - pdb=" SG  CYS K 671 "
        pdb="ZN    ZN K 802 " - pdb=" SG  CYS K 648 "
      pdb="  ZN L 801 "
        pdb="ZN    ZN L 801 " - pdb=" ND1 HIS L 665 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 663 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 683 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 686 "
      pdb="  ZN L 802 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 668 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 648 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 671 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 651 "
      Number of angles added : 18


  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1672

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      65.7% alpha, 3.4% beta
      134 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.712A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 113
      removed outlier: 3.543A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A 108 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   CYS A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.758A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.505A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.700A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.526A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.564A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 35
      removed outlier: 3.666A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.586A  pdb=" N   VAL C  54 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU C  56 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR C  57 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.867A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.604A  pdb=" N   LEU C 116 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.719A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.716A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL D  66 " --> pdb=" O   MET D  62 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLU D  76 " --> pdb=" O   ARG D  72 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA D  77 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 100
      removed outlier: 3.690A  pdb=" N   ARG D  99 " --> pdb=" O   GLN D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.648A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
      removed outlier: 3.789A  pdb=" N   ILE E  51 " --> pdb=" O   ALA E  47 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.561A  pdb=" N   ALA E  95 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER E  96 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASP E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASN E 108 " --> pdb=" O   PHE E 104 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS E 110 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA E 111 " --> pdb=" O   THR E 107 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.989A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU E 126 " --> pdb=" O   LYS E 122 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.885A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.516A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.009A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU F  63 " --> pdb=" O   LYS F  59 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN F  64 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL F  65 " --> pdb=" O   PHE F  61 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE F  66 " --> pdb=" O   LEU F  62 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 4.137A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
      removed outlier: 3.851A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 47 through 73
      removed outlier: 3.978A  pdb=" N   ALA G  53 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL G  54 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLU G  56 " --> pdb=" O   ALA G  52 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR G  57 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR G  59 " --> pdb=" O   LEU G  55 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY G  67 " --> pdb=" O   LEU G  63 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ASN G  68 " --> pdb=" O   GLU G  64 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ALA G  69 " --> pdb=" O   LEU G  65 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 85
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.874A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.685A  pdb=" N   VAL H  66 " --> pdb=" O   MET H  62 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASN H  67 " --> pdb=" O   ASN H  63 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ARG H  79 " --> pdb=" O   GLY H  75 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU H  80 " --> pdb=" O   GLU H  76 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.858A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU H 100 " --> pdb=" O   THR H  96 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 4.317A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS H 116 " --> pdb=" O   SER H 112 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR H 119 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 633 through 647
      removed outlier: 3.758A  pdb=" N   LEU K 645 " --> pdb=" O   ASN K 641 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 668 through 677
      removed outlier: 3.699A  pdb=" N   GLU K 674 " --> pdb=" O   ASN K 670 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG K 675 " --> pdb=" O   CYS K 671 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 691 through 693
      No H-bonds generated for 'chain 'K' and resid 691 through 693'
    Processing helix  chain 'L' and resid 633 through 647
      removed outlier: 4.038A  pdb=" N   GLU L 638 " --> pdb=" O   ALA L 634 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 669 through 678
      removed outlier: 3.732A  pdb=" N   LYS L 673 " --> pdb=" O   GLU L 669 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   GLU L 674 " --> pdb=" O   ASN L 670 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ARG L 675 " --> pdb=" O   CYS L 671 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU L 676 " --> pdb=" O   CYS L 672 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ALA L 678 " --> pdb=" O   GLU L 674 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.586A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98
      removed outlier: 7.074A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.521A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.715A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.853A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.561A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.456A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 666 through 667
    Processing sheet with id=AB1, first strand: chain 'L' and resid 666 through 667

    331 hydrogen bonds defined for protein.
    978 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      696 hydrogen bond angles
      0 basepair planarities
      134 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1754
        1.33 -     1.45: 5009
        1.45 -     1.57: 6430
        1.57 -     1.70: 582
        1.70 -     1.82: 46
  Bond restraints: 13821
  Sorted by residual:
  bond pdb=" CA  ARG A  53 "
       pdb=" C   ARG A  53 "
    ideal  model  delta    sigma   weight residual
    1.524  1.488  0.036 1.29e-02 6.01e+03 7.82e+00
  bond pdb=" C   TYR A  54 "
       pdb=" O   TYR A  54 "
    ideal  model  delta    sigma   weight residual
    1.236  1.201  0.035 1.31e-02 5.83e+03 6.98e+00
  bond pdb=" O3'  DT J 140 "
       pdb=" P    DT J 141 "
    ideal  model  delta    sigma   weight residual
    1.607  1.645 -0.038 1.50e-02 4.44e+03 6.42e+00
  bond pdb=" C   ARG A  53 "
       pdb=" O   ARG A  53 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.028 1.19e-02 7.06e+03 5.70e+00
  bond pdb=" C   LYS H 120 "
       pdb=" O   LYS H 120 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.19e-02 7.06e+03 5.47e+00
  ... (remaining 13816 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 19326
        1.69 -     3.37: 543
        3.37 -     5.06: 37
        5.06 -     6.74: 11
        6.74 -     8.43: 1
  Bond angle restraints: 19918
  Sorted by residual:
  angle pdb=" N   THR L 662 "
        pdb=" CA  THR L 662 "
        pdb=" C   THR L 662 "
      ideal   model   delta    sigma   weight residual
     111.36  117.44   -6.08 1.09e+00 8.42e-01 3.11e+01
  angle pdb=" N   VAL E 117 "
        pdb=" CA  VAL E 117 "
        pdb=" C   VAL E 117 "
      ideal   model   delta    sigma   weight residual
     113.71  108.47    5.24 9.50e-01 1.11e+00 3.05e+01
  angle pdb=" O3'  DC I  78 "
        pdb=" C3'  DC I  78 "
        pdb=" C2'  DC I  78 "
      ideal   model   delta    sigma   weight residual
     111.50  105.03    6.47 1.50e+00 4.44e-01 1.86e+01
  angle pdb=" N   GLY E 132 "
        pdb=" CA  GLY E 132 "
        pdb=" C   GLY E 132 "
      ideal   model   delta    sigma   weight residual
     113.18  121.61   -8.43 2.37e+00 1.78e-01 1.26e+01
  angle pdb=" O3'  DT J  99 "
        pdb=" C3'  DT J  99 "
        pdb=" C2'  DT J  99 "
      ideal   model   delta    sigma   weight residual
     111.50  106.41    5.09 1.50e+00 4.44e-01 1.15e+01
  ... (remaining 19913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.73: 6218
       34.73 -    69.47: 1339
       69.47 -   104.20: 13
      104.20 -   138.93: 0
      138.93 -   173.67: 3
  Dihedral angle restraints: 7573
    sinusoidal: 4993
      harmonic: 2580
  Sorted by residual:
  dihedral pdb=" C4'  DC J 126 "
           pdb=" C3'  DC J 126 "
           pdb=" O3'  DC J 126 "
           pdb=" P    DC J 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.33  173.67     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   31.77 -171.77     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG J  94 "
           pdb=" C3'  DG J  94 "
           pdb=" O3'  DG J  94 "
           pdb=" P    DG J  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   69.84  150.16     1      3.50e+01 8.16e-04 1.46e+01
  ... (remaining 7570 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1971
       0.051 -    0.102: 259
       0.102 -    0.153: 33
       0.153 -    0.204: 3
       0.204 -    0.255: 8
  Chirality restraints: 2274
  Sorted by residual:
  chirality pdb=" CA  ARG E 131 "
            pdb=" N   ARG E 131 "
            pdb=" C   ARG E 131 "
            pdb=" CB  ARG E 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  ASN L 687 "
            pdb=" N   ASN L 687 "
            pdb=" C   ASN L 687 "
            pdb=" CB  ASN L 687 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  THR A  58 "
            pdb=" N   THR A  58 "
            pdb=" C   THR A  58 "
            pdb=" CB  THR A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 2271 not shown)

  Planarity restraints: 1507
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.030 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO E  43 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 100 "    0.020 2.00e-02 2.50e+03   8.27e-03 2.05e+00
        pdb=" N9   DG I 100 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8   DG I 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I 100 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I 100 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I 100 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG I 100 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I 100 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I 100 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I 100 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I 100 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  91 "    0.019 2.00e-02 2.50e+03   8.54e-03 2.00e+00
        pdb=" N9   DA I  91 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8   DA I  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  91 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  91 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DA I  91 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1504 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2808
        2.81 -     3.33: 10768
        3.33 -     3.85: 22906
        3.85 -     4.38: 27597
        4.38 -     4.90: 39616
  Nonbonded interactions: 103695
  Sorted by model distance:
  nonbonded pdb=" N   THR L 662 "
            pdb=" OD2 ASP L 694 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" OE2 GLU A  50 "
            pdb=" NE  ARG B  39 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" N   CYS L 683 "
            pdb=" O   LYS L 688 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   TYR K 647 "
            pdb=" NZ  LYS K 656 "
     model   vdw
     2.369 3.120
  ... (remaining 103690 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 25 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 14 through 117)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 32 through 124)
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.770
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
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      :  0.008   0.628  13837  Z= 0.336
  Angle     :  0.726  44.084  19936  Z= 0.423
  Chirality :  0.039   0.255   2274
  Planarity :  0.003   0.045   1507
  Dihedral  : 26.528 173.667   5901
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  1.21 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.28), residues: 866
  helix: -0.07 (0.23), residues: 539
  sheet: -1.72 (0.98), residues: 30
  loop : -2.09 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 129 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.021   0.001   PHE L 690 
 TRP   0.003   0.001   TRP K 655 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (13821)
  covalent geometry    : angle       0.64171 (19918)
  hydrogen bonds       : bond        0.18345 (  679)
  hydrogen bonds       : angle       4.69384 ( 1674)
  metal coordination   : bond        0.21951 (   16)
  metal coordination   : angle      11.33294 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 252
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 THR cc_start: 0.9382 (t) cc_final: 0.9127 (p)
REVERT: A  120 MET cc_start: 0.7849 (mmm) cc_final: 0.7572 (mtt)
REVERT: B   59 LYS cc_start: 0.9045 (tttm) cc_final: 0.8801 (ttmm)
REVERT: C   73 ASN cc_start: 0.8698 (t0) cc_final: 0.8307 (t0)
REVERT: D   99 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8171 (mtm-85)
REVERT: E   73 GLU cc_start: 0.8130 (tt0) cc_final: 0.7725 (tt0)
REVERT: F   25 ASN cc_start: 0.8842 (m110) cc_final: 0.8523 (m110)
REVERT: F   67 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8297 (ttp-110)
REVERT: H   71 GLU cc_start: 0.7694 (tp30) cc_final: 0.7443 (tp30)
  outliers start: 13
  outliers final: 5
  residues processed: 260
  average time/residue: 0.1890
  time to fit residues: 61.9247
Evaluate side-chains
  197 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 192
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain G residue   90 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:   50.0000
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
B  75 HIS
D  47 GLN
E  68 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN
G 104 GLN
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 670 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.088147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.058115 restraints weight = 29364.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 1.78
r_work: 0.2618 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2486 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9045
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  13837  Z= 0.238
  Angle     :  0.627  14.557  19936  Z= 0.361
  Chirality :  0.038   0.149   2274
  Planarity :  0.005   0.044   1507
  Dihedral  : 29.540 171.691   4180
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 10.19 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.29), residues: 866
  helix:  0.56 (0.23), residues: 562
  sheet: -1.64 (1.18), residues: 20
  loop : -1.97 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  77 
 TYR   0.013   0.001   TYR F  51 
 PHE   0.022   0.002   PHE H  65 
 TRP   0.002   0.000   TRP K 655 
 HIS   0.006   0.002   HIS L 699 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (13821)
  covalent geometry    : angle       0.60520 (19918)
  hydrogen bonds       : bond        0.05877 (  679)
  hydrogen bonds       : angle       2.96280 ( 1674)
  metal coordination   : bond        0.02421 (   16)
  metal coordination   : angle       5.46891 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 194
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8285 (mmm) cc_final: 0.7952 (mtt)
REVERT: C   73 ASN cc_start: 0.8997 (t0) cc_final: 0.8604 (t0)
REVERT: D   85 LYS cc_start: 0.9504 (mmtm) cc_final: 0.9289 (mttp)
REVERT: G   74 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8968 (mttp)
REVERT: K  675 ARG cc_start: 0.8966 (mmm-85) cc_final: 0.8608 (ttt180)
REVERT: L  675 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6479 (mtp-110)
  outliers start: 26
  outliers final: 19
  residues processed: 202
  average time/residue: 0.1736
  time to fit residues: 45.0873
Evaluate side-chains
  205 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   90 ASP
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  649 SER
Chi-restraints excluded: chain K residue  660 ILE
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  691 SER
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain L residue  697 THR
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:   30.0000
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 108 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.1364

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

Flipped N/Q/H residues before XYZ refinement:
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
K 699 HIS
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 670 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.088730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.058838 restraints weight = 29605.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 1.78
r_work: 0.2640 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2506 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9027
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098  13837  Z= 0.166
  Angle     :  0.579  10.776  19936  Z= 0.336
  Chirality :  0.035   0.149   2274
  Planarity :  0.004   0.043   1507
  Dihedral  : 29.485 173.078   4174
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.20 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.29), residues: 866
  helix:  0.93 (0.23), residues: 560
  sheet: -1.64 (1.22), residues: 20
  loop : -1.94 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  35 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.012   0.001   PHE H  65 
 TRP   0.003   0.000   TRP L 655 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13821)
  covalent geometry    : angle       0.55997 (19918)
  hydrogen bonds       : bond        0.04989 (  679)
  hydrogen bonds       : angle       2.83142 ( 1674)
  metal coordination   : bond        0.02658 (   16)
  metal coordination   : angle       4.89170 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8195 (mmm) cc_final: 0.7799 (mtt)
REVERT: C   73 ASN cc_start: 0.8953 (t0) cc_final: 0.8536 (t0)
REVERT: G   74 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8942 (mttp)
REVERT: H  105 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8440 (tm-30)
REVERT: K  657 ASN cc_start: 0.9081 (t0) cc_final: 0.8818 (m-40)
REVERT: K  658 MET cc_start: 0.8991 (tpp) cc_final: 0.8726 (tpp)
REVERT: K  661 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8561 (ptpp)
REVERT: K  674 GLU cc_start: 0.9205 (pp20) cc_final: 0.8950 (pp20)
REVERT: K  675 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8557 (ttt180)
REVERT: L  675 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6639 (mtp-110)
  outliers start: 22
  outliers final: 19
  residues processed: 194
  average time/residue: 0.1650
  time to fit residues: 41.3485
Evaluate side-chains
  201 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   90 ASP
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain K residue  660 ILE
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain L residue  697 THR
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 107 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 108 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 670 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.085964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.055984 restraints weight = 29531.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 1.80
r_work: 0.2558 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2424 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9097
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  13837  Z= 0.303
  Angle     :  0.641  11.229  19936  Z= 0.371
  Chirality :  0.040   0.144   2274
  Planarity :  0.004   0.043   1507
  Dihedral  : 29.663 172.503   4174
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.34 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.29), residues: 866
  helix:  1.00 (0.23), residues: 558
  sheet: -1.69 (1.20), residues: 20
  loop : -2.15 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  77 
 TYR   0.012   0.002   TYR F  51 
 PHE   0.018   0.002   PHE H  65 
 TRP   0.005   0.001   TRP K 655 
 HIS   0.006   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00700 (13821)
  covalent geometry    : angle       0.62383 (19918)
  hydrogen bonds       : bond        0.06543 (  679)
  hydrogen bonds       : angle       3.01751 ( 1674)
  metal coordination   : bond        0.01093 (   16)
  metal coordination   : angle       4.97016 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8389 (mmm) cc_final: 0.7974 (mtt)
REVERT: D   85 LYS cc_start: 0.9559 (mmtm) cc_final: 0.9347 (mttp)
REVERT: F   25 ASN cc_start: 0.9069 (m-40) cc_final: 0.8410 (m110)
REVERT: K  658 MET cc_start: 0.9168 (tpp) cc_final: 0.8745 (tpp)
REVERT: K  661 LYS cc_start: 0.8931 (ptpt) cc_final: 0.8665 (ptpp)
REVERT: K  675 ARG cc_start: 0.9030 (mmm-85) cc_final: 0.8688 (ttt180)
REVERT: K  697 THR cc_start: 0.8761 (p) cc_final: 0.8514 (t)
REVERT: L  675 ARG cc_start: 0.7257 (mtt180) cc_final: 0.6660 (mtp-110)
  outliers start: 25
  outliers final: 21
  residues processed: 195
  average time/residue: 0.1822
  time to fit residues: 45.7822
Evaluate side-chains
  198 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  670 ASN
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain L residue  663 CYS
Chi-restraints excluded: chain L residue  697 THR
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 110 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 670 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.086307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.056482 restraints weight = 29737.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 1.78
r_work: 0.2580 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2447 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9082
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13837  Z= 0.221
  Angle     :  0.600   9.011  19936  Z= 0.349
  Chirality :  0.037   0.140   2274
  Planarity :  0.004   0.045   1507
  Dihedral  : 29.616 174.209   4172
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.55 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.29), residues: 866
  helix:  1.16 (0.23), residues: 558
  sheet: -1.70 (1.19), residues: 20
  loop : -2.05 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  35 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.013   0.001   PHE H  65 
 TRP   0.003   0.001   TRP K 655 
 HIS   0.005   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (13821)
  covalent geometry    : angle       0.58326 (19918)
  hydrogen bonds       : bond        0.05728 (  679)
  hydrogen bonds       : angle       2.87281 ( 1674)
  metal coordination   : bond        0.01272 (   16)
  metal coordination   : angle       4.69715 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 183
  time to evaluate  : 0.360 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.9021 (t0) cc_final: 0.8617 (t0)
REVERT: D   85 LYS cc_start: 0.9540 (mmtm) cc_final: 0.9314 (mttp)
REVERT: F   25 ASN cc_start: 0.8975 (m-40) cc_final: 0.8480 (m110)
REVERT: H  102 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9225 (mp)
REVERT: K  658 MET cc_start: 0.9097 (tpp) cc_final: 0.8792 (tpp)
REVERT: K  661 LYS cc_start: 0.8929 (ptpt) cc_final: 0.8574 (ptpp)
REVERT: K  675 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8687 (ttt180)
REVERT: K  682 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8085 (mmmt)
REVERT: L  675 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7036 (mtp-110)
  outliers start: 27
  outliers final: 20
  residues processed: 195
  average time/residue: 0.1734
  time to fit residues: 43.9488
Evaluate side-chains
  198 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  670 ASN
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain L residue  663 CYS
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 9 optimal weight:    0.4980
   chunk 54 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 108 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.087159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.057462 restraints weight = 29263.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 1.76
r_work: 0.2603 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2473 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9060
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13837  Z= 0.166
  Angle     :  0.584   8.351  19936  Z= 0.340
  Chirality :  0.035   0.137   2274
  Planarity :  0.004   0.041   1507
  Dihedral  : 29.592 175.013   4172
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.09 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.29), residues: 866
  helix:  1.29 (0.23), residues: 563
  sheet: -1.73 (1.21), residues: 20
  loop : -1.99 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 681 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.011   0.001   PHE H  65 
 TRP   0.003   0.001   TRP L 655 
 HIS   0.014   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13821)
  covalent geometry    : angle       0.57030 (19918)
  hydrogen bonds       : bond        0.05177 (  679)
  hydrogen bonds       : angle       2.78643 ( 1674)
  metal coordination   : bond        0.01291 (   16)
  metal coordination   : angle       4.25800 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.9007 (t0) cc_final: 0.8597 (t0)
REVERT: D   85 LYS cc_start: 0.9527 (mmtm) cc_final: 0.9297 (mttp)
REVERT: F   25 ASN cc_start: 0.8932 (m-40) cc_final: 0.8456 (m110)
REVERT: H  113 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8487 (mp0)
REVERT: K  658 MET cc_start: 0.9118 (tpp) cc_final: 0.8801 (tpp)
REVERT: K  674 GLU cc_start: 0.9148 (pp20) cc_final: 0.8894 (pp20)
REVERT: K  675 ARG cc_start: 0.9011 (mmm-85) cc_final: 0.8601 (ttt180)
REVERT: K  682 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8143 (mmmt)
REVERT: L  675 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7101 (mtp-110)
  outliers start: 26
  outliers final: 22
  residues processed: 194
  average time/residue: 0.1682
  time to fit residues: 42.6509
Evaluate side-chains
  203 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  670 ASN
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain L residue  663 CYS
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 99 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN
H  63 ASN
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.085839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.055942 restraints weight = 29691.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 1.79
r_work: 0.2565 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2430 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9095
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  13837  Z= 0.266
  Angle     :  0.615   8.880  19936  Z= 0.358
  Chirality :  0.039   0.146   2274
  Planarity :  0.004   0.042   1507
  Dihedral  : 29.560 174.995   4172
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 15.68 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.29), residues: 866
  helix:  1.31 (0.23), residues: 564
  sheet: -2.27 (1.71), residues: 10
  loop : -1.89 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  35 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.016   0.002   PHE H  65 
 TRP   0.011   0.002   TRP L 655 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 (13821)
  covalent geometry    : angle       0.60189 (19918)
  hydrogen bonds       : bond        0.05987 (  679)
  hydrogen bonds       : angle       2.91015 ( 1674)
  metal coordination   : bond        0.01140 (   16)
  metal coordination   : angle       4.19825 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   85 LYS cc_start: 0.9546 (mmtm) cc_final: 0.9331 (mttp)
REVERT: F   25 ASN cc_start: 0.8953 (m-40) cc_final: 0.8385 (m110)
REVERT: H  113 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8504 (mp0)
REVERT: K  658 MET cc_start: 0.9188 (tpp) cc_final: 0.8862 (tpp)
REVERT: K  661 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8683 (ptpp)
REVERT: K  674 GLU cc_start: 0.9201 (pp20) cc_final: 0.8870 (pp20)
REVERT: K  675 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8628 (ttt180)
REVERT: L  650 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6631 (mt)
REVERT: L  667 PHE cc_start: 0.6500 (m-10) cc_final: 0.6183 (m-80)
  outliers start: 31
  outliers final: 27
  residues processed: 197
  average time/residue: 0.1779
  time to fit residues: 45.2732
Evaluate side-chains
  203 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  670 ASN
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain K residue  695 LEU
Chi-restraints excluded: chain L residue  650 LEU
Chi-restraints excluded: chain L residue  663 CYS
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 107 optimal weight:    8.9990
   chunk 69 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.086960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.057244 restraints weight = 29020.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 1.77
r_work: 0.2602 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2469 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9064
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13837  Z= 0.166
  Angle     :  0.613  15.546  19936  Z= 0.347
  Chirality :  0.036   0.204   2274
  Planarity :  0.005   0.093   1507
  Dihedral  : 29.538 176.286   4172
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 15.82 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.29), residues: 866
  helix:  1.46 (0.23), residues: 564
  sheet: -2.20 (1.75), residues: 10
  loop : -1.85 (0.32), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG L 675 
 TYR   0.019   0.001   TYR K 647 
 PHE   0.011   0.001   PHE L 690 
 TRP   0.007   0.001   TRP L 655 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13821)
  covalent geometry    : angle       0.58514 (19918)
  hydrogen bonds       : bond        0.05067 (  679)
  hydrogen bonds       : angle       2.76017 ( 1674)
  metal coordination   : bond        0.01621 (   16)
  metal coordination   : angle       6.15165 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.9023 (t0) cc_final: 0.8627 (t0)
REVERT: D   85 LYS cc_start: 0.9531 (mmtm) cc_final: 0.9306 (mttp)
REVERT: D  105 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8571 (mp0)
REVERT: E  120 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8989 (mtp)
REVERT: F   25 ASN cc_start: 0.8878 (m-40) cc_final: 0.8436 (m110)
REVERT: H  113 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8461 (mp0)
REVERT: K  658 MET cc_start: 0.9187 (tpp) cc_final: 0.8847 (tpp)
REVERT: K  675 ARG cc_start: 0.8956 (mmm-85) cc_final: 0.8702 (ttt180)
  outliers start: 31
  outliers final: 26
  residues processed: 193
  average time/residue: 0.1643
  time to fit residues: 41.2083
Evaluate side-chains
  205 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  670 ASN
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain L residue  663 CYS
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0000
   chunk 81 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.087571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.057787 restraints weight = 29626.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 1.79
r_work: 0.2614 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.2481 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9052
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13837  Z= 0.169
  Angle     :  0.576   9.834  19936  Z= 0.336
  Chirality :  0.035   0.151   2274
  Planarity :  0.004   0.064   1507
  Dihedral  : 29.464 177.176   4172
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 16.35 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.29), residues: 866
  helix:  1.60 (0.23), residues: 564
  sheet: -2.30 (1.67), residues: 10
  loop : -1.73 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG L 675 
 TYR   0.010   0.001   TYR L 647 
 PHE   0.010   0.001   PHE L 690 
 TRP   0.006   0.001   TRP L 655 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (13821)
  covalent geometry    : angle       0.56602 (19918)
  hydrogen bonds       : bond        0.04722 (  679)
  hydrogen bonds       : angle       2.68799 ( 1674)
  metal coordination   : bond        0.01504 (   16)
  metal coordination   : angle       3.60510 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   85 LYS cc_start: 0.9528 (mmtm) cc_final: 0.9307 (mttp)
REVERT: D  105 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8585 (mp0)
REVERT: E  120 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8963 (mtp)
REVERT: F   25 ASN cc_start: 0.8922 (m-40) cc_final: 0.8484 (m110)
REVERT: H  113 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8461 (mp0)
REVERT: K  658 MET cc_start: 0.9177 (tpp) cc_final: 0.8838 (tpp)
REVERT: K  661 LYS cc_start: 0.8955 (ptpt) cc_final: 0.8482 (ptpt)
REVERT: K  675 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8705 (ttt180)
  outliers start: 28
  outliers final: 25
  residues processed: 196
  average time/residue: 0.1383
  time to fit residues: 35.5122
Evaluate side-chains
  206 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  670 ASN
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain K residue  692 SER
Chi-restraints excluded: chain L residue  647 TYR
Chi-restraints excluded: chain L residue  663 CYS
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 99 optimal weight:   30.0000
   chunk 100 optimal weight:   40.0000
   chunk 42 optimal weight:    0.8980
   chunk 98 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.087758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.058009 restraints weight = 29893.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 1.79
r_work: 0.2622 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.2487 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9047
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13837  Z= 0.175
  Angle     :  0.568  10.117  19936  Z= 0.331
  Chirality :  0.035   0.136   2274
  Planarity :  0.004   0.041   1507
  Dihedral  : 29.421 176.978   4170
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.76 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.29), residues: 866
  helix:  1.60 (0.23), residues: 566
  sheet: -2.49 (1.68), residues: 10
  loop : -1.64 (0.33), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 675 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.010   0.001   PHE H  65 
 TRP   0.004   0.001   TRP L 655 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (13821)
  covalent geometry    : angle       0.55868 (19918)
  hydrogen bonds       : bond        0.04596 (  679)
  hydrogen bonds       : angle       2.64555 ( 1674)
  metal coordination   : bond        0.00984 (   16)
  metal coordination   : angle       3.52290 (   18)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   85 LYS cc_start: 0.9509 (mmtm) cc_final: 0.9287 (mttp)
REVERT: E  120 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8940 (mtp)
REVERT: F   25 ASN cc_start: 0.8903 (m-40) cc_final: 0.8472 (m110)
REVERT: H  113 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8481 (mp0)
REVERT: K  647 TYR cc_start: 0.7712 (m-10) cc_final: 0.7278 (m-80)
REVERT: K  656 LYS cc_start: 0.9014 (mttp) cc_final: 0.8673 (mmtm)
REVERT: K  658 MET cc_start: 0.9163 (tpp) cc_final: 0.8827 (tpp)
REVERT: K  675 ARG cc_start: 0.8956 (mmm-85) cc_final: 0.8599 (ttt180)
  outliers start: 26
  outliers final: 23
  residues processed: 188
  average time/residue: 0.1584
  time to fit residues: 38.7323
Evaluate side-chains
  203 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain K residue  670 ASN
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  647 TYR
Chi-restraints excluded: chain L residue  663 CYS
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.088095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.058401 restraints weight = 29598.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.79
r_work: 0.2631 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2498 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9037
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13837  Z= 0.153
  Angle     :  0.566   9.835  19936  Z= 0.329
  Chirality :  0.034   0.139   2274
  Planarity :  0.004   0.065   1507
  Dihedral  : 29.422 177.027   4170
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.02 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.29), residues: 866
  helix:  1.67 (0.23), residues: 565
  sheet: -2.63 (1.66), residues: 10
  loop : -1.61 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.000   ARG L 675 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.012   0.001   PHE L 667 
 TRP   0.004   0.001   TRP L 655 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13821)
  covalent geometry    : angle       0.55518 (19918)
  hydrogen bonds       : bond        0.04407 (  679)
  hydrogen bonds       : angle       2.62586 ( 1674)
  metal coordination   : bond        0.00954 (   16)
  metal coordination   : angle       3.70813 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3486.12 seconds
wall clock time: 60 minutes 8.68 seconds (3608.68 seconds total)