Starting phenix.real_space_refine
on Wed Jul 30 20:13:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t3y_41016/07_2025/8t3y_41016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t3y_41016/07_2025/8t3y_41016.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t3y_41016/07_2025/8t3y_41016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t3y_41016/07_2025/8t3y_41016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t3y_41016/07_2025/8t3y_41016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t3y_41016/07_2025/8t3y_41016.cif"
  }
  resolution = 3.47
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P     292      5.49       5
     S      32      5.16       5
     C    7249      2.51       5
     N    2425      2.21       5
     O    2999      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13001
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 800
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 543
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "L"
      Number of atoms: 543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 543
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "L"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12166  SG  CYS K 663      94.355  72.816  65.837  1.00139.73           S
  ATOM  12325  SG  CYS K 683      93.142  74.641  62.690  1.00119.37           S
  ATOM  12345  SG  CYS K 686      96.345  72.628  62.545  1.00125.56           S
  ATOM  12049  SG  CYS K 648      85.738  81.611  66.914  1.00162.60           S
  ATOM  12069  SG  CYS K 651      83.084  84.229  67.970  1.00163.36           S
  ATOM  12204  SG  CYS K 668      82.674  80.608  68.908  1.00143.24           S
  ATOM  12227  SG  CYS K 671      81.963  81.360  65.671  1.00136.31           S
  ATOM  12709  SG  CYS L 663      91.116  70.796  85.897  1.00172.78           S
  ATOM  12868  SG  CYS L 683      92.443  70.565  89.900  1.00186.18           S
  ATOM  12888  SG  CYS L 686      89.213  70.114  89.733  1.00190.44           S
  ATOM  12592  SG  CYS L 648     100.439  80.745  85.760  1.00189.02           S
  ATOM  12612  SG  CYS L 651     103.664  82.864  85.645  1.00190.09           S
  ATOM  12747  SG  CYS L 668     103.350  79.634  83.727  1.00189.67           S
  ATOM  12770  SG  CYS L 671     103.665  79.459  87.442  1.00190.98           S

  Time building chain proxies: 8.44, per 1000 atoms: 0.65
  Number of scatterers: 13001
  At special positions: 0
  Unit cell: (127.395, 115.425, 117.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      4     29.99
     S      32     16.00
     P     292     15.00
     O    2999      8.00
     N    2425      7.00
     C    7249      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.99
  Conformation dependent library (CDL) restraints added in 987.2 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 671 "
        pdb="ZN    ZN K 802 " - pdb=" SG  CYS K 651 "
        pdb="ZN    ZN K 802 " - pdb=" SG  CYS K 648 "
      pdb="  ZN L 801 "
        pdb="ZN    ZN L 801 " - pdb=" ND1 HIS L 665 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 663 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 683 "
        pdb="ZN    ZN L 801 " - pdb=" SG  CYS L 686 "
      pdb="  ZN L 802 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 668 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 648 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 671 "
        pdb="ZN    ZN L 802 " - pdb=" SG  CYS L 651 "
      Number of angles added : 18


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

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      65.7% alpha, 3.4% beta
      134 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 5.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.713A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 113
      removed outlier: 3.544A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASN A 108 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   CYS A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.759A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.505A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.701A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.527A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.562A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 35
      removed outlier: 3.665A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.585A  pdb=" N   VAL C  54 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU C  56 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR C  57 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.866A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.604A  pdb=" N   LEU C 116 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.719A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.716A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL D  66 " --> pdb=" O   MET D  62 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLU D  76 " --> pdb=" O   ARG D  72 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA D  77 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 100
      removed outlier: 3.689A  pdb=" N   ARG D  99 " --> pdb=" O   GLN D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.647A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   THR D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
      removed outlier: 3.788A  pdb=" N   ILE E  51 " --> pdb=" O   ALA E  47 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.562A  pdb=" N   ALA E  95 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER E  96 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASN E 108 " --> pdb=" O   PHE E 104 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS E 110 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA E 111 " --> pdb=" O   THR E 107 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.988A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU E 126 " --> pdb=" O   LYS E 122 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.885A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.516A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.009A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLU F  63 " --> pdb=" O   LYS F  59 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN F  64 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL F  65 " --> pdb=" O   PHE F  61 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE F  66 " --> pdb=" O   LEU F  62 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 4.137A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
      removed outlier: 3.851A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 47 through 73
      removed outlier: 3.978A  pdb=" N   ALA G  53 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL G  54 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU G  56 " --> pdb=" O   ALA G  52 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR G  57 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR G  59 " --> pdb=" O   LEU G  55 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLY G  67 " --> pdb=" O   LEU G  63 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ASN G  68 " --> pdb=" O   GLU G  64 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA G  69 " --> pdb=" O   LEU G  65 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 85
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.873A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.686A  pdb=" N   VAL H  66 " --> pdb=" O   MET H  62 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASN H  67 " --> pdb=" O   ASN H  63 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ARG H  79 " --> pdb=" O   GLY H  75 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU H  80 " --> pdb=" O   GLU H  76 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.858A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU H 100 " --> pdb=" O   THR H  96 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 4.318A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS H 116 " --> pdb=" O   SER H 112 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR H 119 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 633 through 647
      removed outlier: 3.758A  pdb=" N   LEU K 645 " --> pdb=" O   ASN K 641 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 668 through 677
      removed outlier: 3.699A  pdb=" N   GLU K 674 " --> pdb=" O   ASN K 670 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG K 675 " --> pdb=" O   CYS K 671 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 691 through 693
      No H-bonds generated for 'chain 'K' and resid 691 through 693'
    Processing helix  chain 'L' and resid 633 through 647
      removed outlier: 4.039A  pdb=" N   GLU L 638 " --> pdb=" O   ALA L 634 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 669 through 678
      removed outlier: 3.732A  pdb=" N   LYS L 673 " --> pdb=" O   GLU L 669 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   GLU L 674 " --> pdb=" O   ASN L 670 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ARG L 675 " --> pdb=" O   CYS L 671 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU L 676 " --> pdb=" O   CYS L 672 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ALA L 678 " --> pdb=" O   GLU L 674 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.587A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98
      removed outlier: 7.073A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.521A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.715A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.852A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.561A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.455A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 666 through 667
    Processing sheet with id=AB1, first strand: chain 'L' and resid 666 through 667

    331 hydrogen bonds defined for protein.
    978 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      696 hydrogen bond angles
      0 basepair planarities
      134 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 4.29

  Time building geometry restraints manager: 3.60 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1728
        1.32 -     1.45: 5025
        1.45 -     1.57: 6440
        1.57 -     1.70: 582
        1.70 -     1.82: 46
  Bond restraints: 13821
  Sorted by residual:
  bond pdb=" CA  ARG A  53 "
       pdb=" C   ARG A  53 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.035 1.29e-02 6.01e+03 7.38e+00
  bond pdb=" C   TYR A  54 "
       pdb=" O   TYR A  54 "
    ideal  model  delta    sigma   weight residual
    1.236  1.201  0.035 1.31e-02 5.83e+03 7.26e+00
  bond pdb=" O3'  DT J 140 "
       pdb=" P    DT J 141 "
    ideal  model  delta    sigma   weight residual
    1.607  1.644 -0.037 1.50e-02 4.44e+03 6.24e+00
  bond pdb=" C   ARG A  53 "
       pdb=" O   ARG A  53 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.029 1.19e-02 7.06e+03 5.92e+00
  bond pdb=" C   LYS H 120 "
       pdb=" O   LYS H 120 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.028 1.19e-02 7.06e+03 5.61e+00
  ... (remaining 13816 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 19334
        1.69 -     3.38: 535
        3.38 -     5.06: 37
        5.06 -     6.75: 11
        6.75 -     8.44: 1
  Bond angle restraints: 19918
  Sorted by residual:
  angle pdb=" N   THR L 662 "
        pdb=" CA  THR L 662 "
        pdb=" C   THR L 662 "
      ideal   model   delta    sigma   weight residual
     111.36  117.42   -6.06 1.09e+00 8.42e-01 3.09e+01
  angle pdb=" N   VAL E 117 "
        pdb=" CA  VAL E 117 "
        pdb=" C   VAL E 117 "
      ideal   model   delta    sigma   weight residual
     113.71  108.49    5.22 9.50e-01 1.11e+00 3.02e+01
  angle pdb=" O3'  DC I  78 "
        pdb=" C3'  DC I  78 "
        pdb=" C2'  DC I  78 "
      ideal   model   delta    sigma   weight residual
     111.50  105.07    6.43 1.50e+00 4.44e-01 1.84e+01
  angle pdb=" N   GLY E 132 "
        pdb=" CA  GLY E 132 "
        pdb=" C   GLY E 132 "
      ideal   model   delta    sigma   weight residual
     113.18  121.62   -8.44 2.37e+00 1.78e-01 1.27e+01
  angle pdb=" O3'  DT J  99 "
        pdb=" C3'  DT J  99 "
        pdb=" C2'  DT J  99 "
      ideal   model   delta    sigma   weight residual
     111.50  106.43    5.07 1.50e+00 4.44e-01 1.14e+01
  ... (remaining 19913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.73: 6216
       34.73 -    69.47: 1341
       69.47 -   104.20: 13
      104.20 -   138.94: 0
      138.94 -   173.67: 3
  Dihedral angle restraints: 7573
    sinusoidal: 4993
      harmonic: 2580
  Sorted by residual:
  dihedral pdb=" C4'  DC J 126 "
           pdb=" C3'  DC J 126 "
           pdb=" O3'  DC J 126 "
           pdb=" P    DC J 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.33  173.67     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   31.72 -171.72     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG J  94 "
           pdb=" C3'  DG J  94 "
           pdb=" O3'  DG J  94 "
           pdb=" P    DG J  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   69.93  150.07     1      3.50e+01 8.16e-04 1.46e+01
  ... (remaining 7570 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1973
       0.052 -    0.104: 258
       0.104 -    0.157: 32
       0.157 -    0.209: 5
       0.209 -    0.261: 6
  Chirality restraints: 2274
  Sorted by residual:
  chirality pdb=" CA  ARG E 131 "
            pdb=" N   ARG E 131 "
            pdb=" C   ARG E 131 "
            pdb=" CB  ARG E 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  ASN L 687 "
            pdb=" N   ASN L 687 "
            pdb=" C   ASN L 687 "
            pdb=" CB  ASN L 687 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  THR A  58 "
            pdb=" N   THR A  58 "
            pdb=" C   THR A  58 "
            pdb=" CB  THR A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 2271 not shown)

  Planarity restraints: 1507
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.030 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO E  43 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 100 "    0.020 2.00e-02 2.50e+03   8.26e-03 2.05e+00
        pdb=" N9   DG I 100 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8   DG I 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I 100 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I 100 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I 100 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG I 100 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I 100 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I 100 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I 100 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  20 "    0.019 2.00e-02 2.50e+03   8.62e-03 2.04e+00
        pdb=" N9   DA I  20 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DA I  20 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DA I  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I  20 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  20 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  20 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  20 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DA I  20 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3   DA I  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DA I  20 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1504 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2801
        2.81 -     3.33: 10764
        3.33 -     3.85: 22906
        3.85 -     4.38: 27619
        4.38 -     4.90: 39610
  Nonbonded interactions: 103700
  Sorted by model distance:
  nonbonded pdb=" N   THR L 662 "
            pdb=" OD2 ASP L 694 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" OE2 GLU A  50 "
            pdb=" NE  ARG B  39 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" N   CYS L 683 "
            pdb=" O   LYS L 688 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   TYR K 647 "
            pdb=" NZ  LYS K 656 "
     model   vdw
     2.370 3.120
  ... (remaining 103695 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.360
  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:          0.570
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     36.410
  Find NCS groups from input model:        0.300
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.628  13837  Z= 0.335
  Angle     :  0.726  44.076  19936  Z= 0.423
  Chirality :  0.039   0.261   2274
  Planarity :  0.003   0.045   1507
  Dihedral  : 26.537 173.671   5901
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  1.21 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.27 (0.28), residues: 866
  helix: -0.07 (0.23), residues: 539
  sheet: -1.72 (0.98), residues: 30
  loop : -2.10 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 655 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.020   0.002   PHE L 690 
 TYR   0.009   0.001   TYR A  54 
 ARG   0.003   0.001   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18344 (  679)
  hydrogen bonds       : angle       4.69391 ( 1674)
  metal coordination   : bond        0.21940 (   16)
  metal coordination   : angle      11.33189 (   18)
  covalent geometry    : bond        0.00374 (13821)
  covalent geometry    : angle       0.64191 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 249
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8419 (mmm) cc_final: 0.7945 (mtt)
REVERT: B   59 LYS cc_start: 0.9028 (tttm) cc_final: 0.8814 (ttpp)
REVERT: E   73 GLU cc_start: 0.7972 (tt0) cc_final: 0.7669 (tt0)
REVERT: F   25 ASN cc_start: 0.9112 (m110) cc_final: 0.8673 (m110)
REVERT: H  113 GLU cc_start: 0.8196 (tp30) cc_final: 0.7984 (tp30)
REVERT: K  647 TYR cc_start: 0.8040 (m-10) cc_final: 0.6852 (m-80)
REVERT: K  658 MET cc_start: 0.8527 (tpp) cc_final: 0.8304 (tpp)
REVERT: K  693 ASN cc_start: 0.9276 (p0) cc_final: 0.9039 (p0)
REVERT: L  693 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6977 (m-40)
REVERT: L  694 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6113 (m-30)
  outliers start: 13
  outliers final: 5
  residues processed: 257
  average time/residue: 0.3816
  time to fit residues: 124.4580
Evaluate side-chains
  177 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain E residue  130 ILE
Chi-restraints excluded: chain G residue   90 ASP
Chi-restraints excluded: chain L residue  693 ASN
Chi-restraints excluded: chain L residue  694 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
B  93 GLN
C 104 GLN
E  68 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN
K 654 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.083577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.054698 restraints weight = 33946.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 2.04
r_work: 0.2540 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  13837  Z= 0.239
  Angle     :  0.626  11.840  19936  Z= 0.361
  Chirality :  0.037   0.129   2274
  Planarity :  0.005   0.043   1507
  Dihedral  : 29.417 172.262   4184
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  8.85 %
    Favored  : 88.47 %
  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: -0.50 (0.29), residues: 866
  helix:  0.54 (0.23), residues: 563
  sheet: -1.91 (1.02), residues: 20
  loop : -1.94 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 655 
 HIS   0.006   0.001   HIS C  31 
 PHE   0.015   0.002   PHE L 690 
 TYR   0.019   0.001   TYR K 647 
 ARG   0.004   0.001   ARG G  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05922 (  679)
  hydrogen bonds       : angle       3.05993 ( 1674)
  metal coordination   : bond        0.01702 (   16)
  metal coordination   : angle       4.51153 (   18)
  covalent geometry    : bond        0.00546 (13821)
  covalent geometry    : angle       0.61155 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 174
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8790 (mmm) cc_final: 0.8414 (mtt)
REVERT: B   84 MET cc_start: 0.9049 (mmt) cc_final: 0.8769 (mmt)
REVERT: C   91 GLU cc_start: 0.7886 (pm20) cc_final: 0.7530 (pm20)
REVERT: C   92 GLU cc_start: 0.8732 (mp0) cc_final: 0.8277 (mp0)
REVERT: D   34 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8923 (mtpt)
REVERT: E   73 GLU cc_start: 0.8777 (tt0) cc_final: 0.8458 (tt0)
REVERT: F   25 ASN cc_start: 0.9306 (m110) cc_final: 0.8770 (m110)
REVERT: F   74 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8562 (tp30)
REVERT: G   90 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8160 (p0)
REVERT: K  647 TYR cc_start: 0.7948 (m-10) cc_final: 0.7691 (m-80)
REVERT: K  658 MET cc_start: 0.8760 (tpp) cc_final: 0.8461 (tpp)
REVERT: K  688 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8527 (mptt)
REVERT: L  655 TRP cc_start: 0.8781 (m100) cc_final: 0.8545 (m100)
REVERT: L  693 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7157 (p0)
  outliers start: 20
  outliers final: 12
  residues processed: 186
  average time/residue: 0.3733
  time to fit residues: 91.2186
Evaluate side-chains
  178 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   90 ASP
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain L residue  657 ASN
Chi-restraints excluded: chain L residue  693 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 98 optimal weight:    7.9990
   chunk 101 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.084184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.055334 restraints weight = 34036.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 2.04
r_work: 0.2558 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13837  Z= 0.182
  Angle     :  0.574  12.006  19936  Z= 0.334
  Chirality :  0.035   0.143   2274
  Planarity :  0.004   0.044   1507
  Dihedral  : 29.339 172.466   4176
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.66 %
    Favored  : 85.39 %
  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: -0.09 (0.29), residues: 866
  helix:  0.92 (0.23), residues: 558
  sheet: -1.51 (1.09), residues: 20
  loop : -1.90 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L 655 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.012   0.002   PHE K 642 
 TYR   0.017   0.001   TYR K 647 
 ARG   0.007   0.000   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04854 (  679)
  hydrogen bonds       : angle       2.80473 ( 1674)
  metal coordination   : bond        0.00668 (   16)
  metal coordination   : angle       4.38426 (   18)
  covalent geometry    : bond        0.00405 (13821)
  covalent geometry    : angle       0.55868 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8761 (mmm) cc_final: 0.8484 (mtp)
REVERT: D   34 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8937 (mtpt)
REVERT: E   73 GLU cc_start: 0.8795 (tt0) cc_final: 0.8439 (tt0)
REVERT: F   25 ASN cc_start: 0.9272 (m110) cc_final: 0.8803 (m110)
REVERT: F   74 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8597 (tp30)
REVERT: K  658 MET cc_start: 0.8869 (tpp) cc_final: 0.8483 (tpp)
REVERT: K  688 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8594 (mptt)
REVERT: L  647 TYR cc_start: 0.8854 (m-80) cc_final: 0.8293 (m-80)
REVERT: L  655 TRP cc_start: 0.8927 (m100) cc_final: 0.8488 (m100)
  outliers start: 22
  outliers final: 18
  residues processed: 178
  average time/residue: 0.3595
  time to fit residues: 83.5228
Evaluate side-chains
  179 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   90 ASP
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  657 ASN
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 102 optimal weight:    7.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
F  27 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
L 654 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.084375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.055665 restraints weight = 33910.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2746 rms_B_bonded: 2.04
r_work: 0.2565 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13837  Z= 0.169
  Angle     :  0.572  12.050  19936  Z= 0.332
  Chirality :  0.034   0.150   2274
  Planarity :  0.004   0.056   1507
  Dihedral  : 29.339 172.576   4172
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.14 %
    Favored  : 83.91 %
  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:  0.19 (0.29), residues: 866
  helix:  1.11 (0.23), residues: 563
  sheet: -1.51 (1.11), residues: 20
  loop : -1.78 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP K 655 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.053   0.002   PHE L 642 
 TYR   0.011   0.001   TYR K 647 
 ARG   0.021   0.000   ARG K 643 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  679)
  hydrogen bonds       : angle       2.70047 ( 1674)
  metal coordination   : bond        0.00738 (   16)
  metal coordination   : angle       4.55454 (   18)
  covalent geometry    : bond        0.00373 (13821)
  covalent geometry    : angle       0.55533 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8761 (mmm) cc_final: 0.8463 (mtp)
REVERT: C   91 GLU cc_start: 0.7763 (pm20) cc_final: 0.7200 (pm20)
REVERT: C   92 GLU cc_start: 0.8628 (mp0) cc_final: 0.7953 (mp0)
REVERT: D   34 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8966 (mtpt)
REVERT: D  105 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8580 (mp0)
REVERT: E   73 GLU cc_start: 0.8803 (tt0) cc_final: 0.8564 (tt0)
REVERT: F   25 ASN cc_start: 0.9222 (m110) cc_final: 0.8768 (m110)
REVERT: F   74 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8654 (tp30)
REVERT: G   90 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8275 (p0)
REVERT: K  642 PHE cc_start: 0.7668 (m-80) cc_final: 0.7008 (m-80)
REVERT: K  643 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6855 (mmm160)
REVERT: K  647 TYR cc_start: 0.8509 (m-80) cc_final: 0.8070 (m-80)
REVERT: K  658 MET cc_start: 0.8904 (tpp) cc_final: 0.8504 (tpp)
REVERT: K  691 SER cc_start: 0.7910 (t) cc_final: 0.7601 (p)
REVERT: L  647 TYR cc_start: 0.8844 (m-80) cc_final: 0.8442 (m-80)
REVERT: L  655 TRP cc_start: 0.8943 (m100) cc_final: 0.8691 (m100)
  outliers start: 22
  outliers final: 17
  residues processed: 180
  average time/residue: 0.3357
  time to fit residues: 79.4024
Evaluate side-chains
  183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  105 GLU
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   90 ASP
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  657 ASN
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 108 optimal weight:   30.0000
   chunk 81 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0470
   overall best weight:    1.1082

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  31 HIS
L 654 ASN
L 670 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.084819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.056155 restraints weight = 34197.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 2.04
r_work: 0.2582 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13837  Z= 0.159
  Angle     :  0.563  11.361  19936  Z= 0.325
  Chirality :  0.034   0.154   2274
  Planarity :  0.003   0.038   1507
  Dihedral  : 29.306 172.886   4172
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 13.54 %
    Favored  : 83.24 %
  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:  0.47 (0.29), residues: 866
  helix:  1.34 (0.23), residues: 563
  sheet: -1.55 (1.12), residues: 20
  loop : -1.67 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP L 655 
 HIS   0.007   0.001   HIS L 699 
 PHE   0.032   0.002   PHE L 642 
 TYR   0.005   0.001   TYR F  51 
 ARG   0.014   0.000   ARG L 643 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04282 (  679)
  hydrogen bonds       : angle       2.60306 ( 1674)
  metal coordination   : bond        0.00790 (   16)
  metal coordination   : angle       4.94099 (   18)
  covalent geometry    : bond        0.00347 (13821)
  covalent geometry    : angle       0.54321 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 176
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8723 (mmm) cc_final: 0.8406 (mtp)
REVERT: C   91 GLU cc_start: 0.7795 (pm20) cc_final: 0.7257 (pm20)
REVERT: C   92 GLU cc_start: 0.8658 (mp0) cc_final: 0.7900 (mp0)
REVERT: D   34 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8963 (mtpt)
REVERT: E   73 GLU cc_start: 0.8800 (tt0) cc_final: 0.8527 (tt0)
REVERT: F   25 ASN cc_start: 0.9208 (m110) cc_final: 0.8770 (m110)
REVERT: F   54 THR cc_start: 0.9684 (m) cc_final: 0.9484 (m)
REVERT: K  647 TYR cc_start: 0.8486 (m-80) cc_final: 0.8186 (m-80)
REVERT: K  658 MET cc_start: 0.8978 (tpp) cc_final: 0.8565 (tpp)
REVERT: K  699 HIS cc_start: 0.7583 (m90) cc_final: 0.7264 (m-70)
REVERT: L  647 TYR cc_start: 0.8798 (m-80) cc_final: 0.8392 (m-80)
REVERT: L  661 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8826 (mttp)
  outliers start: 24
  outliers final: 20
  residues processed: 187
  average time/residue: 0.3816
  time to fit residues: 93.6652
Evaluate side-chains
  189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  657 ASN
Chi-restraints excluded: chain L residue  662 THR
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 106 optimal weight:   20.0000
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
F  75 HIS
L 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.085480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.056818 restraints weight = 34454.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 2.06
r_work: 0.2598 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13837  Z= 0.149
  Angle     :  0.561  10.714  19936  Z= 0.322
  Chirality :  0.034   0.164   2274
  Planarity :  0.004   0.039   1507
  Dihedral  : 29.278 173.337   4170
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.75 %
    Favored  : 82.44 %
  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:  0.73 (0.29), residues: 866
  helix:  1.53 (0.23), residues: 566
  sheet: -1.47 (1.15), residues: 20
  loop : -1.58 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L 655 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.043   0.002   PHE L 642 
 TYR   0.015   0.001   TYR L 647 
 ARG   0.012   0.000   ARG K 643 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  679)
  hydrogen bonds       : angle       2.53656 ( 1674)
  metal coordination   : bond        0.00703 (   16)
  metal coordination   : angle       4.96595 (   18)
  covalent geometry    : bond        0.00322 (13821)
  covalent geometry    : angle       0.54073 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8661 (mmm) cc_final: 0.8351 (mtp)
REVERT: C   92 GLU cc_start: 0.8688 (mp0) cc_final: 0.8469 (mp0)
REVERT: D   34 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8965 (mtpt)
REVERT: E   73 GLU cc_start: 0.8822 (tt0) cc_final: 0.8547 (tt0)
REVERT: F   25 ASN cc_start: 0.9187 (m110) cc_final: 0.8759 (m110)
REVERT: K  642 PHE cc_start: 0.7800 (m-80) cc_final: 0.7468 (m-80)
REVERT: K  645 LEU cc_start: 0.8971 (mt) cc_final: 0.8727 (tp)
REVERT: K  647 TYR cc_start: 0.8377 (m-80) cc_final: 0.8039 (m-80)
REVERT: K  658 MET cc_start: 0.8950 (tpp) cc_final: 0.8540 (tpp)
REVERT: K  699 HIS cc_start: 0.7547 (m90) cc_final: 0.7243 (m-70)
REVERT: L  647 TYR cc_start: 0.8745 (m-80) cc_final: 0.8378 (m-80)
REVERT: L  661 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8875 (mttp)
REVERT: L  688 LYS cc_start: 0.9330 (mttt) cc_final: 0.8795 (tptp)
  outliers start: 21
  outliers final: 17
  residues processed: 188
  average time/residue: 0.3337
  time to fit residues: 83.3024
Evaluate side-chains
  185 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
E  68 GLN
L 654 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.083612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.054788 restraints weight = 34146.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 2.05
r_work: 0.2541 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13837  Z= 0.206
  Angle     :  0.593  11.258  19936  Z= 0.340
  Chirality :  0.036   0.164   2274
  Planarity :  0.004   0.039   1507
  Dihedral  : 29.346 172.042   4170
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.88 %
    Favored  : 82.04 %
  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:  0.76 (0.29), residues: 866
  helix:  1.54 (0.22), residues: 570
  sheet: -1.43 (1.16), residues: 20
  loop : -1.59 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L 655 
 HIS   0.006   0.001   HIS L 699 
 PHE   0.043   0.002   PHE L 642 
 TYR   0.011   0.001   TYR L 647 
 ARG   0.011   0.000   ARG K 643 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04945 (  679)
  hydrogen bonds       : angle       2.71412 ( 1674)
  metal coordination   : bond        0.00722 (   16)
  metal coordination   : angle       5.00331 (   18)
  covalent geometry    : bond        0.00465 (13821)
  covalent geometry    : angle       0.57340 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8833 (mmm) cc_final: 0.8444 (mtt)
REVERT: D   34 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8997 (mtpt)
REVERT: E   73 GLU cc_start: 0.8808 (tt0) cc_final: 0.8608 (tt0)
REVERT: F   25 ASN cc_start: 0.9173 (m110) cc_final: 0.8682 (m110)
REVERT: K  642 PHE cc_start: 0.7826 (m-80) cc_final: 0.7312 (m-80)
REVERT: K  645 LEU cc_start: 0.8963 (mt) cc_final: 0.8705 (tp)
REVERT: K  658 MET cc_start: 0.8958 (tpp) cc_final: 0.8726 (tpp)
REVERT: K  688 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8676 (mptt)
REVERT: K  699 HIS cc_start: 0.7793 (m90) cc_final: 0.7364 (m-70)
REVERT: L  647 TYR cc_start: 0.8760 (m-80) cc_final: 0.8333 (m-80)
REVERT: L  661 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8875 (mttp)
REVERT: L  688 LYS cc_start: 0.9341 (mttt) cc_final: 0.8761 (tptp)
  outliers start: 23
  outliers final: 20
  residues processed: 179
  average time/residue: 0.3644
  time to fit residues: 86.7884
Evaluate side-chains
  183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9990
   chunk 107 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 102 optimal weight:   20.0000
   chunk 25 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
L 654 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.084253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.055583 restraints weight = 34160.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 2.06
r_work: 0.2562 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13837  Z= 0.163
  Angle     :  0.577  11.055  19936  Z= 0.331
  Chirality :  0.034   0.170   2274
  Planarity :  0.004   0.037   1507
  Dihedral  : 29.320 172.921   4170
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.28 %
    Favored  : 81.77 %
  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:  0.84 (0.29), residues: 866
  helix:  1.60 (0.22), residues: 572
  sheet: -1.44 (1.14), residues: 20
  loop : -1.57 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 655 
 HIS   0.005   0.001   HIS L 699 
 PHE   0.037   0.002   PHE L 642 
 TYR   0.007   0.001   TYR L 647 
 ARG   0.010   0.000   ARG K 643 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04446 (  679)
  hydrogen bonds       : angle       2.60583 ( 1674)
  metal coordination   : bond        0.00726 (   16)
  metal coordination   : angle       4.96590 (   18)
  covalent geometry    : bond        0.00360 (13821)
  covalent geometry    : angle       0.55797 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8754 (mmm) cc_final: 0.8336 (mtt)
REVERT: F   25 ASN cc_start: 0.9131 (m110) cc_final: 0.8672 (m110)
REVERT: K  642 PHE cc_start: 0.7765 (m-80) cc_final: 0.7215 (m-80)
REVERT: K  645 LEU cc_start: 0.8908 (mt) cc_final: 0.8621 (tp)
REVERT: K  658 MET cc_start: 0.9009 (tpp) cc_final: 0.8769 (tpp)
REVERT: K  699 HIS cc_start: 0.7764 (m90) cc_final: 0.7349 (m-70)
REVERT: L  647 TYR cc_start: 0.8773 (m-80) cc_final: 0.8341 (m-80)
REVERT: L  661 LYS cc_start: 0.9102 (ttmt) cc_final: 0.8859 (mttp)
REVERT: L  688 LYS cc_start: 0.9315 (mttt) cc_final: 0.8673 (tptp)
  outliers start: 22
  outliers final: 21
  residues processed: 176
  average time/residue: 0.3703
  time to fit residues: 86.7395
Evaluate side-chains
  187 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 72 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
L 654 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.082787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.053953 restraints weight = 34079.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.2703 rms_B_bonded: 2.05
r_work: 0.2519 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13837  Z= 0.226
  Angle     :  0.612   9.835  19936  Z= 0.352
  Chirality :  0.037   0.174   2274
  Planarity :  0.004   0.037   1507
  Dihedral  : 29.381 171.654   4170
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.01 %
    Favored  : 81.77 %
  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:  0.74 (0.29), residues: 866
  helix:  1.54 (0.22), residues: 569
  sheet: -1.67 (1.12), residues: 20
  loop : -1.59 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L 655 
 HIS   0.005   0.001   HIS L 699 
 PHE   0.032   0.002   PHE L 642 
 TYR   0.007   0.001   TYR F  72 
 ARG   0.009   0.001   ARG K 643 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05298 (  679)
  hydrogen bonds       : angle       2.76463 ( 1674)
  metal coordination   : bond        0.00832 (   16)
  metal coordination   : angle       4.94164 (   18)
  covalent geometry    : bond        0.00515 (13821)
  covalent geometry    : angle       0.59365 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8855 (mmm) cc_final: 0.8061 (mtt)
REVERT: A  123 ASP cc_start: 0.9128 (m-30) cc_final: 0.8918 (m-30)
REVERT: B   84 MET cc_start: 0.9170 (mmm) cc_final: 0.8969 (mmt)
REVERT: C   91 GLU cc_start: 0.8017 (pm20) cc_final: 0.7805 (pm20)
REVERT: C   92 GLU cc_start: 0.8747 (mp0) cc_final: 0.8374 (mp0)
REVERT: F   25 ASN cc_start: 0.9103 (m110) cc_final: 0.8498 (m-40)
REVERT: K  642 PHE cc_start: 0.7831 (m-80) cc_final: 0.7283 (m-80)
REVERT: K  645 LEU cc_start: 0.8922 (mt) cc_final: 0.8634 (tp)
REVERT: K  658 MET cc_start: 0.9020 (tpp) cc_final: 0.8670 (tpp)
REVERT: K  687 ASN cc_start: 0.9162 (t0) cc_final: 0.8928 (t0)
REVERT: K  688 LYS cc_start: 0.9247 (mmmm) cc_final: 0.9002 (mmmm)
REVERT: K  699 HIS cc_start: 0.7849 (m90) cc_final: 0.7423 (m-70)
REVERT: L  647 TYR cc_start: 0.8837 (m-80) cc_final: 0.8420 (m-80)
REVERT: L  688 LYS cc_start: 0.9327 (mttt) cc_final: 0.8653 (tptp)
  outliers start: 24
  outliers final: 22
  residues processed: 176
  average time/residue: 0.3676
  time to fit residues: 85.6572
Evaluate side-chains
  184 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
L 654 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.081254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.052106 restraints weight = 33915.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.2657 rms_B_bonded: 2.09
r_work: 0.2467 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046  13837  Z= 0.304
  Angle     :  0.673  12.202  19936  Z= 0.382
  Chirality :  0.040   0.164   2274
  Planarity :  0.005   0.037   1507
  Dihedral  : 29.464 170.439   4170
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.95 %
    Favored  : 81.10 %
  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:  0.45 (0.29), residues: 866
  helix:  1.36 (0.22), residues: 566
  sheet: -2.01 (1.16), residues: 20
  loop : -1.76 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L 655 
 HIS   0.007   0.001   HIS K 699 
 PHE   0.025   0.002   PHE L 642 
 TYR   0.010   0.001   TYR F  72 
 ARG   0.006   0.001   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06272 (  679)
  hydrogen bonds       : angle       3.01258 ( 1674)
  metal coordination   : bond        0.01105 (   16)
  metal coordination   : angle       5.54500 (   18)
  covalent geometry    : bond        0.00702 (13821)
  covalent geometry    : angle       0.65208 (19918)

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

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 1.639 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8878 (mmm) cc_final: 0.8194 (mtt)
REVERT: B   84 MET cc_start: 0.9191 (mmm) cc_final: 0.8970 (mmt)
REVERT: C   73 ASN cc_start: 0.9012 (t0) cc_final: 0.8617 (t0)
REVERT: F   25 ASN cc_start: 0.9148 (m110) cc_final: 0.8653 (m-40)
REVERT: K  642 PHE cc_start: 0.7811 (m-80) cc_final: 0.7497 (p90)
REVERT: K  645 LEU cc_start: 0.8908 (mt) cc_final: 0.8540 (tp)
REVERT: K  647 TYR cc_start: 0.8297 (m-80) cc_final: 0.8045 (m-80)
REVERT: K  658 MET cc_start: 0.9102 (tpp) cc_final: 0.8767 (tpp)
REVERT: K  687 ASN cc_start: 0.9229 (t0) cc_final: 0.9000 (t0)
REVERT: K  688 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9081 (mmmm)
REVERT: K  699 HIS cc_start: 0.7812 (m90) cc_final: 0.7480 (m-70)
REVERT: L  647 TYR cc_start: 0.8826 (m-80) cc_final: 0.8399 (m-80)
REVERT: L  688 LYS cc_start: 0.9340 (mttt) cc_final: 0.8651 (tptp)
  outliers start: 22
  outliers final: 22
  residues processed: 172
  average time/residue: 0.4617
  time to fit residues: 105.4987
Evaluate side-chains
  179 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 2.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue  676 LEU
Chi-restraints excluded: chain L residue  654 ASN
Chi-restraints excluded: chain L residue  698 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 92 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 99 optimal weight:   20.0000
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
L 654 ASN
L 657 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.082167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.053328 restraints weight = 34050.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2687 rms_B_bonded: 2.04
r_work: 0.2502 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13837  Z= 0.198
  Angle     :  0.627  13.640  19936  Z= 0.357
  Chirality :  0.036   0.169   2274
  Planarity :  0.004   0.037   1507
  Dihedral  : 29.417 172.262   4170
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.68 %
    Favored  : 81.10 %
  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:  0.53 (0.29), residues: 866
  helix:  1.42 (0.22), residues: 569
  sheet: -2.06 (1.15), residues: 20
  loop : -1.75 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP L 655 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.027   0.002   PHE L 642 
 TYR   0.009   0.001   TYR L 647 
 ARG   0.007   0.000   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05263 (  679)
  hydrogen bonds       : angle       2.80341 ( 1674)
  metal coordination   : bond        0.00818 (   16)
  metal coordination   : angle       5.70106 (   18)
  covalent geometry    : bond        0.00448 (13821)
  covalent geometry    : angle       0.60354 (19918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6979.01 seconds
wall clock time: 125 minutes 50.03 seconds (7550.03 seconds total)