Starting phenix.real_space_refine
on Wed Jul 30 19:58:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t3t_41011/07_2025/8t3t_41011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t3t_41011/07_2025/8t3t_41011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2025/8t3t_41011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2025/8t3t_41011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2025/8t3t_41011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2025/8t3t_41011.cif"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.015
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    7243      2.51       5
     N    2423      2.21       5
     O    2997      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12991
  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: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    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  12156  SG  CYS K 663      99.375  75.126  80.380  1.00227.89           S
  ATOM  12315  SG  CYS K 683     101.649  76.294  83.194  1.00249.62           S
  ATOM  12335  SG  CYS K 686      98.552  74.224  84.036  1.00253.88           S
  ATOM  12039  SG  CYS K 648     105.375  86.157  77.237  1.00280.67           S
  ATOM  12059  SG  CYS K 651     107.516  88.976  76.374  1.00289.30           S
  ATOM  12194  SG  CYS K 668     108.042  85.897  74.379  1.00267.32           S
  ATOM  12217  SG  CYS K 671     109.223  85.686  77.834  1.00266.56           S
  ATOM  12699  SG  CYS L 663      95.659  76.176  60.519  1.00160.31           S
  ATOM  12858  SG  CYS L 683      92.975  77.494  58.092  1.00136.58           S
  ATOM  12878  SG  CYS L 686      96.246  76.198  56.724  1.00148.23           S
  ATOM  12582  SG  CYS L 648      85.727  83.231  65.188  1.00193.20           S
  ATOM  12602  SG  CYS L 651      82.289  84.005  66.644  1.00193.10           S
  ATOM  12737  SG  CYS L 668      83.899  80.805  67.477  1.00167.52           S
  ATOM  12760  SG  CYS L 671      82.719  80.984  64.086  1.00156.96           S

  Time building chain proxies: 9.04, per 1000 atoms: 0.70
  Number of scatterers: 12991
  At special positions: 0
  Unit cell: (129.96, 119.7, 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    2997      8.00
     N    2423      7.00
     C    7243      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: 2.92
  Conformation dependent library (CDL) restraints added in 914.4 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 686 "
        pdb="ZN    ZN K 801 " - pdb=" SG  CYS K 663 "
      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 648 "
        pdb="ZN    ZN K 802 " - pdb=" SG  CYS K 671 "
      pdb="  ZN L 801 "
        pdb="ZN    ZN L 801 " - pdb=" ND1 HIS L 665 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 683 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 686 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 663 "
      pdb="  ZN L 802 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 668 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 651 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 648 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 671 "
      Number of angles added : 18


  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1670

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 12 sheets defined
      66.7% alpha, 3.6% beta
      133 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 5.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 55
      removed outlier: 3.684A  pdb=" N   ILE A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.574A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.786A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASN A 108 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   CYS A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.940A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 50 through 76
      removed outlier: 3.816A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL B  65 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.887A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.581A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TYR C  57 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE C  62 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU C  63 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLU C  64 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP C  72 " --> pdb=" O   ASN C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.607A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.509A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU C  97 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.834A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.781A  pdb=" N   SER D  60 " --> pdb=" O   SER D  56 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   MET D  62 " --> pdb=" O   ALA D  58 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER D  64 " --> pdb=" O   SER D  60 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASN D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.758A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.594A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 64 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.750A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU E  97 " --> pdb=" O   GLN E  93 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   TYR E  99 " --> pdb=" O   ALA E  95 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU E 100 " --> pdb=" O   SER E  96 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.598A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.927A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLU F  63 " --> pdb=" O   LYS F  59 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN F  64 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL F  65 " --> pdb=" O   PHE F  61 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.530A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.514A  pdb=" N   VAL G  54 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.856A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.703A  pdb=" N   GLU H  76 " --> pdb=" O   ARG H  72 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA H  77 " --> pdb=" O   ILE H  73 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG H  79 " --> pdb=" O   GLY H  75 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.608A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG H  99 " --> pdb=" O   GLN H  95 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
      removed outlier: 3.756A  pdb=" N   ALA H 107 " --> pdb=" O   PRO H 103 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 633 through 647
    Processing helix  chain 'K' and resid 668 through 678
      removed outlier: 3.893A  pdb=" N   CYS K 672 " --> pdb=" O   CYS K 668 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LYS K 673 " --> pdb=" O   GLU K 669 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU K 674 " --> pdb=" O   ASN K 670 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 633 through 647
      removed outlier: 3.592A  pdb=" N   TYR L 647 " --> pdb=" O   ARG L 643 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 668 through 677
      removed outlier: 3.654A  pdb=" N   GLU L 674 " --> pdb=" O   ASN L 670 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 691 through 693
      No H-bonds generated for 'chain 'L' and resid 691 through 693'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.970A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.523A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 3.673A  pdb=" N   THR G 101 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.250A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.891A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.021A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.580A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.136A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 666 through 667
    Processing sheet with id=AB3, first strand: chain 'L' and resid 666 through 667

    364 hydrogen bonds defined for protein.
    1065 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      342 hydrogen bonds
      684 hydrogen bond angles
      0 basepair planarities
      133 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 4.36

  Time building geometry restraints manager: 3.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3057
        1.34 -     1.46: 4223
        1.46 -     1.58: 5903
        1.58 -     1.70: 582
        1.70 -     1.82: 46
  Bond restraints: 13811
  Sorted by residual:
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.92e+00
  bond pdb=" N   GLY D  53 "
       pdb=" CA  GLY D  53 "
    ideal  model  delta    sigma   weight residual
    1.442  1.451 -0.009 7.70e-03 1.69e+04 1.46e+00
  bond pdb=" N   ASN K 687 "
       pdb=" CA  ASN K 687 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.25e+00
  bond pdb=" CA  ASP E  81 "
       pdb=" CB  ASP E  81 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.21e+00
  bond pdb=" C3'  DG J  94 "
       pdb=" O3'  DG J  94 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.18e+00
  ... (remaining 13806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 19482
        1.82 -     3.64: 387
        3.64 -     5.45: 29
        5.45 -     7.27: 5
        7.27 -     9.09: 2
  Bond angle restraints: 19905
  Sorted by residual:
  angle pdb=" CA  GLU L 669 "
        pdb=" CB  GLU L 669 "
        pdb=" CG  GLU L 669 "
      ideal   model   delta    sigma   weight residual
     114.10  121.86   -7.76 2.00e+00 2.50e-01 1.51e+01
  angle pdb=" CA  GLY D  53 "
        pdb=" C   GLY D  53 "
        pdb=" N   ILE D  54 "
      ideal   model   delta    sigma   weight residual
     114.65  117.96   -3.31 9.20e-01 1.18e+00 1.30e+01
  angle pdb=" O3'  DG J 137 "
        pdb=" C3'  DG J 137 "
        pdb=" C2'  DG J 137 "
      ideal   model   delta    sigma   weight residual
     111.50  106.47    5.03 1.50e+00 4.44e-01 1.12e+01
  angle pdb=" C   THR E  80 "
        pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
      ideal   model   delta    sigma   weight residual
     121.54  127.86   -6.32 1.91e+00 2.74e-01 1.10e+01
  angle pdb=" CA  LYS K 661 "
        pdb=" CB  LYS K 661 "
        pdb=" CG  LYS K 661 "
      ideal   model   delta    sigma   weight residual
     114.10  120.70   -6.60 2.00e+00 2.50e-01 1.09e+01
  ... (remaining 19900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.18: 5811
       30.18 -    60.35: 1716
       60.35 -    90.53: 35
       90.53 -   120.70: 0
      120.70 -   150.88: 3
  Dihedral angle restraints: 7565
    sinusoidal: 4988
      harmonic: 2577
  Sorted by residual:
  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   69.12  150.88     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" CA  CYS L 686 "
           pdb=" C   CYS L 686 "
           pdb=" N   ASN L 687 "
           pdb=" CA  ASN L 687 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.85   19.15     0      5.00e+00 4.00e-02 1.47e+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    2.57 -142.57     1      3.50e+01 8.16e-04 1.41e+01
  ... (remaining 7562 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1718
       0.037 -    0.074: 450
       0.074 -    0.111: 86
       0.111 -    0.148: 18
       0.148 -    0.185: 1
  Chirality restraints: 2273
  Sorted by residual:
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.54e-01
  chirality pdb=" CA  ASP E  77 "
            pdb=" N   ASP E  77 "
            pdb=" C   ASP E  77 "
            pdb=" CB  ASP E  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ASN K 687 "
            pdb=" N   ASN K 687 "
            pdb=" C   ASN K 687 "
            pdb=" CB  ASN K 687 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 2270 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP K 694 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.39e+00
        pdb=" C   ASP K 694 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASP K 694 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU K 695 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 117 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.87e+00
        pdb=" C   ALA D 117 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ALA D 117 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL D 118 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU L 669 "    0.009 2.00e-02 2.50e+03   1.93e-02 3.74e+00
        pdb=" CD  GLU L 669 "   -0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLU L 669 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU L 669 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1146
        2.74 -     3.28: 11111
        3.28 -     3.82: 22524
        3.82 -     4.36: 27629
        4.36 -     4.90: 40823
  Nonbonded interactions: 103233
  Sorted by model distance:
  nonbonded pdb=" N4   DC I  11 "
            pdb=" N2   DG J 137 "
     model   vdw
     2.202 3.200
  nonbonded pdb=" OG1 THR A  80 "
            pdb=" OD1 ASP A  81 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   TYR K 647 "
            pdb=" NZ  LYS K 656 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" N   LYS K 661 "
            pdb=" OD1 ASP K 694 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   TYR L 647 "
            pdb=" NZ  LYS L 656 "
     model   vdw
     2.265 3.120
  ... (remaining 103228 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'
}
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:             3.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     37.140
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13827  Z= 0.169
  Angle     :  0.613   9.090  19923  Z= 0.366
  Chirality :  0.035   0.185   2273
  Planarity :  0.004   0.033   1505
  Dihedral  : 27.438 150.879   5895
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 27.52 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.28), residues: 865
  helix:  1.24 (0.23), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.83 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 655 
 HIS   0.006   0.001   HIS C  82 
 PHE   0.012   0.001   PHE H  65 
 TYR   0.007   0.001   TYR F  51 
 ARG   0.004   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14052 (  706)
  hydrogen bonds       : angle       4.57560 ( 1749)
  metal coordination   : bond        0.00674 (   16)
  metal coordination   : angle       4.64044 (   18)
  covalent geometry    : bond        0.00361 (13811)
  covalent geometry    : angle       0.59694 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 170
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 170
  average time/residue: 0.3876
  time to fit residues: 84.9755
Evaluate side-chains
  171 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0000
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0870
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:   50.0000
   overall best weight:    1.1566

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
F  75 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.098734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.063771 restraints weight = 27342.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 1.74
r_work: 0.2684 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work: 0.2547 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9032
moved from start:          0.0798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13827  Z= 0.166
  Angle     :  0.552   7.053  19923  Z= 0.328
  Chirality :  0.034   0.148   2273
  Planarity :  0.004   0.035   1505
  Dihedral  : 29.277 150.635   4170
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 24.56 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.29), residues: 865
  helix:  1.73 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -1.79 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K 655 
 HIS   0.005   0.001   HIS C  82 
 PHE   0.007   0.001   PHE D  70 
 TYR   0.007   0.001   TYR C  50 
 ARG   0.003   0.000   ARG C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04894 (  706)
  hydrogen bonds       : angle       2.62374 ( 1749)
  metal coordination   : bond        0.00576 (   16)
  metal coordination   : angle       4.08643 (   18)
  covalent geometry    : bond        0.00365 (13811)
  covalent geometry    : angle       0.53865 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8546 (t0)
REVERT: L  675 ARG cc_start: 0.9320 (mmm160) cc_final: 0.8648 (mmm160)
REVERT: L  694 ASP cc_start: 0.8603 (m-30) cc_final: 0.8182 (m-30)
  outliers start: 16
  outliers final: 9
  residues processed: 177
  average time/residue: 0.3793
  time to fit residues: 87.4009
Evaluate side-chains
  179 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 169
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.098312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.063165 restraints weight = 27524.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 1.73
r_work: 0.2668 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work: 0.2528 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9047
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13827  Z= 0.181
  Angle     :  0.551   6.555  19923  Z= 0.326
  Chirality :  0.035   0.139   2273
  Planarity :  0.004   0.034   1505
  Dihedral  : 29.338 150.061   4168
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 24.70 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.29), residues: 865
  helix:  1.88 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.69 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP L 655 
 HIS   0.004   0.001   HIS C  82 
 PHE   0.009   0.001   PHE L 667 
 TYR   0.007   0.001   TYR F  51 
 ARG   0.002   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04918 (  706)
  hydrogen bonds       : angle       2.52935 ( 1749)
  metal coordination   : bond        0.00762 (   16)
  metal coordination   : angle       4.11944 (   18)
  covalent geometry    : bond        0.00407 (13811)
  covalent geometry    : angle       0.53744 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  694 ASP cc_start: 0.8734 (t0) cc_final: 0.8306 (t0)
REVERT: L  658 MET cc_start: 0.8601 (tpp) cc_final: 0.8252 (tpp)
REVERT: L  694 ASP cc_start: 0.8642 (m-30) cc_final: 0.8195 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 182
  average time/residue: 0.3742
  time to fit residues: 87.8958
Evaluate side-chains
  188 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain K residue  657 ASN
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0020
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0000
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.099110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.064119 restraints weight = 27092.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 1.73
r_work: 0.2693 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2554 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9023
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13827  Z= 0.143
  Angle     :  0.543   6.942  19923  Z= 0.323
  Chirality :  0.034   0.178   2273
  Planarity :  0.003   0.034   1505
  Dihedral  : 29.339 150.590   4168
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 24.16 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.29), residues: 865
  helix:  2.02 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.71 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 655 
 HIS   0.002   0.001   HIS C  82 
 PHE   0.007   0.001   PHE D  70 
 TYR   0.008   0.001   TYR C  50 
 ARG   0.003   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  706)
  hydrogen bonds       : angle       2.48208 ( 1749)
  metal coordination   : bond        0.01079 (   16)
  metal coordination   : angle       3.65923 (   18)
  covalent geometry    : bond        0.00298 (13811)
  covalent geometry    : angle       0.53153 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   42 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7944 (ptm160)
REVERT: G   73 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8524 (t0)
REVERT: K  694 ASP cc_start: 0.8671 (t0) cc_final: 0.8385 (t0)
REVERT: L  669 GLU cc_start: 0.8592 (tp30) cc_final: 0.8361 (tm-30)
REVERT: L  673 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8672 (mmtt)
REVERT: L  694 ASP cc_start: 0.8633 (m-30) cc_final: 0.8159 (m-30)
  outliers start: 23
  outliers final: 16
  residues processed: 193
  average time/residue: 0.3621
  time to fit residues: 90.5255
Evaluate side-chains
  194 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain K residue  657 ASN
Chi-restraints excluded: chain K residue  662 THR
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
Chi-restraints excluded: chain L residue  697 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0020
   chunk 100 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  75 HIS
E  68 GLN
F  25 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.099382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.064441 restraints weight = 27516.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 1.74
r_work: 0.2702 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2562 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9014
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13827  Z= 0.151
  Angle     :  0.531   6.840  19923  Z= 0.316
  Chirality :  0.034   0.167   2273
  Planarity :  0.003   0.034   1505
  Dihedral  : 29.292 149.939   4168
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.49 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.29), residues: 865
  helix:  2.15 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.64 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 655 
 HIS   0.003   0.001   HIS C  82 
 PHE   0.007   0.001   PHE D  70 
 TYR   0.007   0.001   TYR C  50 
 ARG   0.004   0.000   ARG L 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04191 (  706)
  hydrogen bonds       : angle       2.39909 ( 1749)
  metal coordination   : bond        0.00834 (   16)
  metal coordination   : angle       3.68365 (   18)
  covalent geometry    : bond        0.00329 (13811)
  covalent geometry    : angle       0.51988 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 173
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   42 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7952 (ptm160)
REVERT: G   73 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8580 (t0)
REVERT: H   95 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8609 (tt0)
REVERT: L  673 LYS cc_start: 0.8994 (mtmm) cc_final: 0.7843 (mtmm)
REVERT: L  687 ASN cc_start: 0.9128 (t0) cc_final: 0.8895 (t0)
REVERT: L  694 ASP cc_start: 0.8664 (m-30) cc_final: 0.8165 (m-30)
  outliers start: 27
  outliers final: 16
  residues processed: 190
  average time/residue: 0.4024
  time to fit residues: 99.1205
Evaluate side-chains
  191 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   95 GLN
Chi-restraints excluded: chain K residue  662 THR
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
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 14 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 82 optimal weight:    5.9990
   chunk 71 optimal weight:   20.0000
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    2.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.096363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.060757 restraints weight = 27454.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 1.73
r_work: 0.2610 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work: 0.2469 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9096
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  13827  Z= 0.267
  Angle     :  0.609   8.115  19923  Z= 0.356
  Chirality :  0.039   0.187   2273
  Planarity :  0.004   0.034   1505
  Dihedral  : 29.466 149.292   4168
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 23.76 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 865
  helix:  1.93 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.72 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K 655 
 HIS   0.004   0.001   HIS C  31 
 PHE   0.012   0.002   PHE D  70 
 TYR   0.009   0.001   TYR H 121 
 ARG   0.004   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06264 (  706)
  hydrogen bonds       : angle       2.71545 ( 1749)
  metal coordination   : bond        0.01250 (   16)
  metal coordination   : angle       4.53753 (   18)
  covalent geometry    : bond        0.00617 (13811)
  covalent geometry    : angle       0.59347 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6338 (mp0)
REVERT: G   42 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7939 (ptm160)
REVERT: G   73 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8689 (t0)
REVERT: L  673 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8592 (mtmt)
REVERT: L  687 ASN cc_start: 0.9245 (t0) cc_final: 0.9010 (t0)
REVERT: L  694 ASP cc_start: 0.8643 (m-30) cc_final: 0.8134 (m-30)
  outliers start: 31
  outliers final: 25
  residues processed: 191
  average time/residue: 0.3766
  time to fit residues: 92.5836
Evaluate side-chains
  199 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain K residue  662 THR
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
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 24 optimal weight:    3.9990
   chunk 109 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 103 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.1582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.097415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.062099 restraints weight = 27129.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 1.74
r_work: 0.2638 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2497 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9071
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13827  Z= 0.167
  Angle     :  0.586   8.394  19923  Z= 0.343
  Chirality :  0.035   0.183   2273
  Planarity :  0.004   0.033   1505
  Dihedral  : 29.473 150.326   4168
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 24.03 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.29), residues: 865
  helix:  2.01 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.70 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 655 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.009   0.001   PHE D  65 
 TYR   0.008   0.001   TYR C  50 
 ARG   0.003   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05391 (  706)
  hydrogen bonds       : angle       2.63151 ( 1749)
  metal coordination   : bond        0.01272 (   16)
  metal coordination   : angle       4.70246 (   18)
  covalent geometry    : bond        0.00367 (13811)
  covalent geometry    : angle       0.56897 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 172
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   42 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7985 (ptm160)
REVERT: G   73 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8658 (t0)
REVERT: H   95 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8626 (tt0)
REVERT: K  694 ASP cc_start: 0.8456 (t0) cc_final: 0.8227 (t0)
REVERT: L  669 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: L  673 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8506 (mtmt)
REVERT: L  687 ASN cc_start: 0.9237 (t0) cc_final: 0.8976 (t0)
REVERT: L  694 ASP cc_start: 0.8636 (m-30) cc_final: 0.8116 (m-30)
  outliers start: 28
  outliers final: 22
  residues processed: 190
  average time/residue: 0.3853
  time to fit residues: 95.0462
Evaluate side-chains
  196 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   95 GLN
Chi-restraints excluded: chain K residue  662 THR
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
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 87 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   chunk 55 optimal weight:    0.0470
   chunk 90 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 106 optimal weight:   20.0000
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    3.6086

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.095245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.059779 restraints weight = 27222.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 1.72
r_work: 0.2577 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2437 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9118
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048  13827  Z= 0.342
  Angle     :  0.660   8.422  19923  Z= 0.383
  Chirality :  0.042   0.214   2273
  Planarity :  0.004   0.033   1505
  Dihedral  : 29.596 150.495   4168
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 23.76 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.28), residues: 865
  helix:  1.78 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -1.79 (0.31), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K 655 
 HIS   0.005   0.001   HIS E 113 
 PHE   0.015   0.002   PHE H  65 
 TYR   0.010   0.002   TYR D  37 
 ARG   0.004   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07115 (  706)
  hydrogen bonds       : angle       2.89118 ( 1749)
  metal coordination   : bond        0.01281 (   16)
  metal coordination   : angle       4.56087 (   18)
  covalent geometry    : bond        0.00795 (13811)
  covalent geometry    : angle       0.64558 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6229 (mp0)
REVERT: G   42 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7945 (ptm160)
REVERT: G   73 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8686 (t0)
REVERT: K  694 ASP cc_start: 0.8473 (t0) cc_final: 0.8238 (t0)
REVERT: L  669 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8330 (tm-30)
REVERT: L  673 LYS cc_start: 0.8844 (mtmm) cc_final: 0.8546 (mtmt)
REVERT: L  687 ASN cc_start: 0.9301 (t0) cc_final: 0.9058 (t0)
REVERT: L  694 ASP cc_start: 0.8681 (m-30) cc_final: 0.8158 (m-30)
  outliers start: 32
  outliers final: 26
  residues processed: 188
  average time/residue: 0.4175
  time to fit residues: 100.6638
Evaluate side-chains
  198 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 169
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain K residue  662 THR
Chi-restraints excluded: chain K residue  698 VAL
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
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 56 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 99 optimal weight:   40.0000
   chunk 0 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 107 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
L 654 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.096817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.061432 restraints weight = 27127.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 1.74
r_work: 0.2642 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work: 0.2504 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9085
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13827  Z= 0.165
  Angle     :  0.610   9.567  19923  Z= 0.358
  Chirality :  0.037   0.192   2273
  Planarity :  0.004   0.040   1505
  Dihedral  : 29.600 151.786   4168
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 23.49 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.28), residues: 865
  helix:  1.90 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.77 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 655 
 HIS   0.002   0.001   HIS C  82 
 PHE   0.008   0.001   PHE D  70 
 TYR   0.011   0.001   TYR C  50 
 ARG   0.004   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05713 (  706)
  hydrogen bonds       : angle       2.71921 ( 1749)
  metal coordination   : bond        0.01338 (   16)
  metal coordination   : angle       4.56808 (   18)
  covalent geometry    : bond        0.00354 (13811)
  covalent geometry    : angle       0.59504 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 1.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6279 (mp0)
REVERT: G   42 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7979 (ptm160)
REVERT: G   73 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8649 (t0)
REVERT: H   95 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: K  657 ASN cc_start: 0.8665 (p0) cc_final: 0.8155 (p0)
REVERT: K  658 MET cc_start: 0.7464 (tpt) cc_final: 0.6140 (tmm)
REVERT: K  694 ASP cc_start: 0.8375 (t0) cc_final: 0.8139 (t0)
REVERT: L  669 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8268 (tm-30)
REVERT: L  673 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8555 (mtmt)
REVERT: L  687 ASN cc_start: 0.9294 (t0) cc_final: 0.9069 (t0)
REVERT: L  694 ASP cc_start: 0.8660 (m-30) cc_final: 0.8117 (m-30)
  outliers start: 31
  outliers final: 23
  residues processed: 190
  average time/residue: 0.5741
  time to fit residues: 141.0722
Evaluate side-chains
  199 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   95 GLN
Chi-restraints excluded: chain K residue  662 THR
Chi-restraints excluded: chain L residue  666 VAL
Chi-restraints excluded: chain L residue  676 LEU
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 26 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.097263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.061969 restraints weight = 27227.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 1.74
r_work: 0.2637 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2498 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13827  Z= 0.167
  Angle     :  0.598  11.757  19923  Z= 0.350
  Chirality :  0.036   0.192   2273
  Planarity :  0.004   0.055   1505
  Dihedral  : 29.527 151.866   4168
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.30 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.29), residues: 865
  helix:  2.01 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.77 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP K 655 
 HIS   0.003   0.001   HIS C  82 
 PHE   0.007   0.001   PHE H  65 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.009   0.000   ARG L 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05189 (  706)
  hydrogen bonds       : angle       2.62350 ( 1749)
  metal coordination   : bond        0.01270 (   16)
  metal coordination   : angle       4.71191 (   18)
  covalent geometry    : bond        0.00362 (13811)
  covalent geometry    : angle       0.58147 (19905)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 169
  time to evaluate  : 2.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6302 (mp0)
REVERT: G   42 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8040 (ptm160)
REVERT: G   73 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8660 (t0)
REVERT: H   95 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8661 (tt0)
REVERT: K  657 ASN cc_start: 0.8627 (p0) cc_final: 0.8155 (p0)
REVERT: K  694 ASP cc_start: 0.8431 (t0) cc_final: 0.8186 (t0)
REVERT: L  669 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: L  673 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8615 (mtmt)
REVERT: L  687 ASN cc_start: 0.9296 (t0) cc_final: 0.9054 (t0)
REVERT: L  694 ASP cc_start: 0.8671 (m-30) cc_final: 0.8134 (m-30)
  outliers start: 26
  outliers final: 21
  residues processed: 185
  average time/residue: 0.5003
  time to fit residues: 119.5794
Evaluate side-chains
  194 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 169
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   95 GLN
Chi-restraints excluded: chain K residue  662 THR
Chi-restraints excluded: chain L residue  666 VAL
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 15 optimal weight:    0.4980
   chunk 109 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0060
   chunk 76 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0770
   chunk 106 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.4554

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.097912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.062800 restraints weight = 27351.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 1.75
r_work: 0.2660 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work: 0.2520 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9053
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13827  Z= 0.150
  Angle     :  0.595  12.299  19923  Z= 0.346
  Chirality :  0.035   0.184   2273
  Planarity :  0.004   0.037   1505
  Dihedral  : 29.508 152.305   4168
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 24.56 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.28), residues: 865
  helix:  2.08 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.72 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP L 655 
 HIS   0.003   0.001   HIS L 665 
 PHE   0.006   0.001   PHE L 642 
 TYR   0.009   0.001   TYR C  50 
 ARG   0.004   0.000   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04709 (  706)
  hydrogen bonds       : angle       2.55930 ( 1749)
  metal coordination   : bond        0.01005 (   16)
  metal coordination   : angle       4.87981 (   18)
  covalent geometry    : bond        0.00314 (13811)
  covalent geometry    : angle       0.57715 (19905)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8594.56 seconds
wall clock time: 155 minutes 23.94 seconds (9323.94 seconds total)