Starting phenix.real_space_refine
on Sat Sep 12 11:00:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bxt_30237/09_2026/7bxt_30237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bxt_30237/09_2026/7bxt_30237.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bxt_30237/09_2026/7bxt_30237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bxt_30237/09_2026/7bxt_30237.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bxt_30237/09_2026/7bxt_30237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bxt_30237/09_2026/7bxt_30237.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P     289      5.49       5
     S      28      5.16       5
     C    9015      2.51       5
     N    2927      2.21       5
     O    3437      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15696
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 854
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
    Chain: "B"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 827
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 737
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 854
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
    Chain: "F"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 737
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2953
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2989
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 174
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "L"
      Number of atoms: 174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 174
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "M"
      Number of atoms: 1645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1645
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 191}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 1651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1651
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 6, 'TRANS': 191}
          Chain breaks: 1
  Time building chain proxies: 3.32, per 1000 atoms: 0.21
  Number of scatterers: 15696
  At special positions: 0
  Unit cell: (124.95, 152.88, 116.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P     289     15.00
     O    3437      8.00
     N    2927      7.00
     C    9015      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: 1.34
  Conformation dependent library (CDL) restraints added in 510.5 milliseconds
  

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 8 sheets defined
      56.8% alpha, 6.8% beta
      146 base pairs and 214 stacking pairs defined.
    Time for finding SS restraints: 2.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 64 through 80
      removed outlier: 3.936A  pdb=" N   ILE A  75 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   CYS A  76 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU A  77 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 117
      removed outlier: 3.591A  pdb=" N   LEU A  92 " --> pdb=" O   GLN A  88 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LEU A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   HIS A 105 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A 117 " --> pdb=" O   CYS A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.535A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.694A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 94
      removed outlier: 4.411A  pdb=" N   ALA B  89 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 34
    Processing helix  chain 'C' and resid 46 through 64
    Processing helix  chain 'C' and resid 67 through 74
      removed outlier: 4.285A  pdb=" N   ASP C  72 " --> pdb=" O   ASN C  68 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 88
      removed outlier: 3.546A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 95
    Processing helix  chain 'D' and resid 37 through 47
      removed outlier: 3.648A  pdb=" N   LYS D  46 " --> pdb=" O   TYR D  42 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 65
    Processing helix  chain 'D' and resid 65 through 84
      removed outlier: 4.350A  pdb=" N   GLU D  71 " --> pdb=" O   ASN D  67 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.782A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU D 102 " --> pdb=" O   VAL D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 121
      removed outlier: 3.688A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 56
      removed outlier: 3.838A  pdb=" N   LEU E  49 " --> pdb=" O   GLY E  45 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ARG E  50 " --> pdb=" O   THR E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 80
      removed outlier: 4.083A  pdb=" N   ILE E  75 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   CYS E  76 " --> pdb=" O   VAL E  72 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU E  77 " --> pdb=" O   ARG E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 117
      removed outlier: 3.955A  pdb=" N   GLU E 100 " --> pdb=" O   GLN E  96 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   HIS E 105 " --> pdb=" O   ALA E 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 133
    Processing helix  chain 'F' and resid 32 through 39
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.905A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 4.403A  pdb=" N   ALA F  89 " --> pdb=" O   ASP F  85 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.243A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA G  53 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP G  72 " --> pdb=" O   ASN G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 88
      removed outlier: 3.751A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 95
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.753A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 4.045A  pdb=" N   VAL H  66 " --> pdb=" O   MET H  62 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ASN H  67 " --> pdb=" O   ASN H  63 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.780A  pdb=" N   GLN H  95 " --> pdb=" O   SER H  91 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   THR H  96 " --> pdb=" O   ARG H  92 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA H  97 " --> pdb=" O   GLU H  93 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU H 102 " --> pdb=" O   VAL H  98 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 106 through 123
      removed outlier: 4.188A  pdb=" N   LYS H 116 " --> pdb=" O   SER H 112 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 15
      removed outlier: 3.774A  pdb=" N   VAL M   6 " --> pdb=" O   ASP M   2 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS M  15 " --> pdb=" O   ARG M  11 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 17 through 19
      No H-bonds generated for 'chain 'M' and resid 17 through 19'
    Processing helix  chain 'M' and resid 20 through 29
    Processing helix  chain 'M' and resid 32 through 37
    Processing helix  chain 'M' and resid 44 through 59
    Processing helix  chain 'M' and resid 62 through 77
    Processing helix  chain 'M' and resid 102 through 111
      removed outlier: 3.885A  pdb=" N   ARG M 108 " --> pdb=" O   LYS M 104 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ARG M 109 " --> pdb=" O   LYS M 105 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLN M 110 " --> pdb=" O   LYS M 106 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE M 111 " --> pdb=" O   PHE M 107 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 170 through 182
    Processing helix  chain 'N' and resid 3 through 14
    Processing helix  chain 'N' and resid 20 through 29
    Processing helix  chain 'N' and resid 32 through 37
    Processing helix  chain 'N' and resid 44 through 60
    Processing helix  chain 'N' and resid 63 through 77
      removed outlier: 3.513A  pdb=" N   ALA N  67 " --> pdb=" O   LEU N  63 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 101 through 112
    Processing helix  chain 'N' and resid 170 through 182
    Processing helix  chain 'N' and resid 196 through 207
      removed outlier: 3.838A  pdb=" N   LEU N 200 " --> pdb=" O   CYS N 196 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 7.322A  pdb=" N   ARG A  86 " --> 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: 6.447A  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 77 through 78
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA5, first strand: chain 'E' and resid 86 through 87
      removed outlier: 7.641A  pdb=" N   ARG E  86 " --> 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 'G' and resid 42 through 43
      removed outlier: 7.371A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'M' and resid 119 through 124
      removed outlier: 3.659A  pdb=" N   THR M 119 " --> pdb=" O   ALA M 135 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   HIS M 154 " --> pdb=" O   TYR M 159 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   TYR M 159 " --> pdb=" O   HIS M 154 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL M  85 " --> pdb=" O   LEU M 192 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   LEU M 192 " --> pdb=" O   VAL M  85 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   HIS M  87 " --> pdb=" O   MET M 190 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   MET M 190 " --> pdb=" O   HIS M  87 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   ASN M  89 " --> pdb=" O   HIS M 188 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   HIS M 188 " --> pdb=" O   ASN M  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 119 through 124
      removed outlier: 3.947A  pdb=" N   TYR N 150 " --> pdb=" O   SER N 163 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   HIS N 154 " --> pdb=" O   TYR N 159 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   TYR N 159 " --> pdb=" O   HIS N 154 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   VAL N  85 " --> pdb=" O   LEU N 192 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   LEU N 192 " --> pdb=" O   VAL N  85 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   HIS N  87 " --> pdb=" O   MET N 190 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   MET N 190 " --> pdb=" O   HIS N  87 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   ASN N  89 " --> pdb=" O   HIS N 188 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   HIS N 188 " --> pdb=" O   ASN N  89 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      372 hydrogen bonds
      732 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      214 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3442
        1.33 -     1.45: 4947
        1.45 -     1.57: 7576
        1.57 -     1.69: 577
        1.69 -     1.81: 46
  Bond restraints: 16588
  Sorted by residual:
  bond pdb=" C3'  DG J 245 "
       pdb=" O3'  DG J 245 "
    ideal  model  delta    sigma   weight residual
    1.435  1.375  0.060 1.30e-02 5.92e+03 2.13e+01
  bond pdb=" C3'  DG I 100 "
       pdb=" O3'  DG I 100 "
    ideal  model  delta    sigma   weight residual
    1.435  1.378  0.057 1.30e-02 5.92e+03 1.95e+01
  bond pdb=" C3'  DC I  69 "
       pdb=" O3'  DC I  69 "
    ideal  model  delta    sigma   weight residual
    1.435  1.381  0.054 1.30e-02 5.92e+03 1.74e+01
  bond pdb=" C3'  DA I  48 "
       pdb=" O3'  DA I  48 "
    ideal  model  delta    sigma   weight residual
    1.435  1.381  0.054 1.30e-02 5.92e+03 1.70e+01
  bond pdb=" C3'  DG J 214 "
       pdb=" O3'  DG J 214 "
    ideal  model  delta    sigma   weight residual
    1.435  1.387  0.048 1.30e-02 5.92e+03 1.34e+01
  ... (remaining 16583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 23030
        2.67 -     5.33: 564
        5.33 -     8.00: 39
        8.00 -    10.67: 10
       10.67 -    13.33: 3
  Bond angle restraints: 23646
  Sorted by residual:
  angle pdb=" O4'  DC I 109 "
        pdb=" C4'  DC I 109 "
        pdb=" C3'  DC I 109 "
      ideal   model   delta    sigma   weight residual
     106.00  101.98    4.02 6.00e-01 2.78e+00 4.48e+01
  angle pdb=" O4'  DT I  67 "
        pdb=" C4'  DT I  67 "
        pdb=" C3'  DT I  67 "
      ideal   model   delta    sigma   weight residual
     106.00  102.04    3.96 6.00e-01 2.78e+00 4.36e+01
  angle pdb=" C   VAL L 654 "
        pdb=" N   ARG L 655 "
        pdb=" CA  ARG L 655 "
      ideal   model   delta    sigma   weight residual
     122.44  114.72    7.72 1.19e+00 7.06e-01 4.20e+01
  angle pdb=" O4'  DG I 131 "
        pdb=" C4'  DG I 131 "
        pdb=" C3'  DG I 131 "
      ideal   model   delta    sigma   weight residual
     106.00  102.43    3.57 6.00e-01 2.78e+00 3.54e+01
  angle pdb=" O4'  DA I  19 "
        pdb=" C4'  DA I  19 "
        pdb=" C3'  DA I  19 "
      ideal   model   delta    sigma   weight residual
     106.00  102.61    3.39 6.00e-01 2.78e+00 3.20e+01
  ... (remaining 23641 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.32: 6711
       24.32 -    48.64: 1659
       48.64 -    72.96: 794
       72.96 -    97.27: 67
       97.27 -   121.59: 1
  Dihedral angle restraints: 9232
    sinusoidal: 5710
      harmonic: 3522
  Sorted by residual:
  dihedral pdb=" CA  ARG L 661 "
           pdb=" C   ARG L 661 "
           pdb=" N   LEU L 662 "
           pdb=" CA  LEU L 662 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.69  -28.31     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  GLU C  92 "
           pdb=" C   GLU C  92 "
           pdb=" N   LEU C  93 "
           pdb=" CA  LEU C  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  ALA H 117 "
           pdb=" C   ALA H 117 "
           pdb=" N   VAL H 118 "
           pdb=" CA  VAL H 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 9229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 2058
       0.067 -    0.133: 519
       0.133 -    0.200: 78
       0.200 -    0.266: 3
       0.266 -    0.333: 1
  Chirality restraints: 2659
  Sorted by residual:
  chirality pdb=" CB  ILE M 134 "
            pdb=" CA  ILE M 134 "
            pdb=" CG1 ILE M 134 "
            pdb=" CG2 ILE M 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" CB  ILE H  54 "
            pdb=" CA  ILE H  54 "
            pdb=" CG1 ILE H  54 "
            pdb=" CG2 ILE H  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CB  ILE N 130 "
            pdb=" CA  ILE N 130 "
            pdb=" CG1 ILE N 130 "
            pdb=" CG2 ILE N 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 2656 not shown)

  Planarity restraints: 1979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR K 667 "   -0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   TYR K 667 "    0.060 2.00e-02 2.50e+03
        pdb=" O   TYR K 667 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   TRP K 668 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR L 667 "    0.017 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   TYR L 667 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   TYR L 667 "    0.022 2.00e-02 2.50e+03
        pdb=" N   TRP L 668 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS L 663 "    0.052 5.00e-02 4.00e+02   7.80e-02 9.74e+00
        pdb=" N   PRO L 664 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO L 664 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO L 664 "    0.044 5.00e-02 4.00e+02
  ... (remaining 1976 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 14
        2.31 -     2.96: 6885
        2.96 -     3.60: 26831
        3.60 -     4.25: 40274
        4.25 -     4.90: 59246
  Nonbonded interactions: 133250
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS H 109 "
            pdb=" O   LYS K 658 "
     model   vdw
     1.659 3.120
  nonbonded pdb=" OE2 GLU G  61 "
            pdb=" OG1 THR K 657 "
     model   vdw
     1.915 3.040
  nonbonded pdb=" CD2 HIS H 109 "
            pdb=" O   LYS K 658 "
     model   vdw
     2.039 3.260
  nonbonded pdb=" OE1 GLU C  64 "
            pdb=" NH2 ARG L 661 "
     model   vdw
     2.126 3.120
  nonbonded pdb=" ND2 ASN C  38 "
            pdb=" OE2 GLU G  41 "
     model   vdw
     2.143 3.120
  ... (remaining 133245 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'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and (resid 11 through 64 or resid 66 through 118))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'M'
  selection = (chain 'N' and (resid 1 through 206 or (resid 207 and (name N or name CA or name \ 
 C or name O or name CB ))))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.610
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:1.240
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
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      :  0.010   0.068  16588  Z= 0.765
  Angle     :  1.031  13.331  23646  Z= 0.788
  Chirality :  0.058   0.333   2659
  Planarity :  0.008   0.078   1979
  Dihedral  : 28.647 121.593   6954
  Min Nonbonded Distance : 1.659

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 12.74 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.26 (0.19), residues: 1171
  helix: -2.98 (0.13), residues: 668
  sheet: -0.91 (0.53), residues: 82
  loop : -2.65 (0.27), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 659 
 TYR   0.023   0.003   TYR H  42 
 PHE   0.017   0.003   PHE B  61 
 TRP   0.014   0.003   TRP K 668 
 HIS   0.010   0.002   HIS N 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01010 /  0.77 (16588)
  covalent geometry    : angle       1.03098 /  0.79 (23646)
  hydrogen bonds       : bond        0.14426 /  9.54 (  837)
  hydrogen bonds       : angle       5.98525 /  4.06 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 357
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7955 (mm-30)
REVERT: A   74 GLU cc_start: 0.8193 (tt0) cc_final: 0.7126 (tt0)
REVERT: A  105 HIS cc_start: 0.8107 (m-70) cc_final: 0.7808 (m170)
REVERT: B   25 ASN cc_start: 0.8303 (t0) cc_final: 0.7551 (t0)
REVERT: C   24 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7600 (tp40)
REVERT: C   34 LEU cc_start: 0.9483 (tp) cc_final: 0.8906 (tp)
REVERT: C   43 VAL cc_start: 0.9414 (t) cc_final: 0.9169 (t)
REVERT: C   87 ILE cc_start: 0.9714 (mm) cc_final: 0.9462 (mt)
REVERT: C   99 ARG cc_start: 0.7320 (ptt-90) cc_final: 0.6755 (ptp-170)
REVERT: D   57 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8761 (mptt)
REVERT: D   71 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7853 (tm-30)
REVERT: D   83 TYR cc_start: 0.8580 (m-10) cc_final: 0.8065 (m-10)
REVERT: D   85 LYS cc_start: 0.8783 (mttt) cc_final: 0.8550 (mmtt)
REVERT: D  121 TYR cc_start: 0.9199 (t80) cc_final: 0.8920 (t80)
REVERT: E  108 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: E  111 TYR cc_start: 0.9487 (t80) cc_final: 0.9283 (t80)
REVERT: E  123 TYR cc_start: 0.8930 (m-80) cc_final: 0.8442 (m-10)
REVERT: E  139 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: F   25 ASN cc_start: 0.7509 (t0) cc_final: 0.6049 (t0)
REVERT: G   38 ASN cc_start: 0.8572 (t0) cc_final: 0.8204 (p0)
REVERT: G   95 LYS cc_start: 0.8699 (tttm) cc_final: 0.8153 (ttmm)
REVERT: H   51 ASP cc_start: 0.8020 (m-30) cc_final: 0.7699 (t0)
REVERT: H   57 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8779 (mptt)
REVERT: H   59 MET cc_start: 0.8914 (tpp) cc_final: 0.8432 (tpp)
REVERT: K  665 LEU cc_start: 0.8793 (tt) cc_final: 0.8534 (tt)
REVERT: M    3 GLU cc_start: 0.8607 (mp0) cc_final: 0.8046 (mp0)
REVERT: M   20 GLU cc_start: 0.8360 (mp0) cc_final: 0.7535 (mp0)
REVERT: M   35 GLN cc_start: 0.8191 (mt0) cc_final: 0.7811 (mt0)
REVERT: M   46 GLU cc_start: 0.7954 (pp20) cc_final: 0.7466 (pp20)
REVERT: M   50 HIS cc_start: 0.8986 (m-70) cc_final: 0.7956 (m-70)
REVERT: M   74 ASN cc_start: 0.8854 (m-40) cc_final: 0.8574 (m-40)
REVERT: M   79 ASN cc_start: 0.8825 (m-40) cc_final: 0.8054 (t0)
REVERT: M  183 ASN cc_start: 0.8441 (m110) cc_final: 0.7819 (p0)
REVERT: M  191 GLU cc_start: 0.8269 (pm20) cc_final: 0.8047 (pm20)
REVERT: N   19 ASP cc_start: 0.8641 (m-30) cc_final: 0.8439 (m-30)
REVERT: N   22 MET cc_start: 0.8204 (mpp) cc_final: 0.7999 (mpp)
REVERT: N   30 PHE cc_start: 0.8448 (t80) cc_final: 0.8216 (t80)
REVERT: N  204 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8202 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 361
  average time/residue: 0.1610
  time to fit residues: 80.4452
Evaluate side-chains
  231 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 229
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  96 GLN
A 137 GLN
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 HIS
C  73 ASN
D  63 ASN
D  84 ASN
D 109 HIS
E  40 HIS
E  96 GLN
** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
G 110 ASN
H  49 HIS
H  63 ASN
H  82 HIS
H  84 ASN
M 112 GLN
M 128 ASN
M 144 ASN
N  50 HIS
N 128 ASN
N 170 ASN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.076332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.058499 restraints weight = 52927.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.058932 restraints weight = 37365.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059229 restraints weight = 33571.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.059429 restraints weight = 27330.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.059491 restraints weight = 24906.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16588  Z= 0.179
  Angle     :  0.759   7.196  23646  Z= 0.424
  Chirality :  0.053   0.242   2659
  Planarity :  0.006   0.081   1979
  Dihedral  : 32.511 116.631   4522
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.31 %
    Favored  : 94.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.22), residues: 1171
  helix: -1.41 (0.18), residues: 667
  sheet: -0.90 (0.51), residues: 84
  loop : -2.36 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  92 
 TYR   0.023   0.002   TYR A 111 
 PHE   0.021   0.003   PHE M 122 
 TRP   0.022   0.002   TRP L 668 
 HIS   0.009   0.002   HIS N  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.18 (16588)
  covalent geometry    : angle       0.75888 /  0.42 (23646)
  hydrogen bonds       : bond        0.06168 /  4.09 (  837)
  hydrogen bonds       : angle       4.17354 /  2.88 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 315
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 GLN cc_start: 0.8252 (mm-40) cc_final: 0.8040 (mm-40)
REVERT: A  137 GLN cc_start: 0.7824 (mm110) cc_final: 0.7574 (mp10)
REVERT: C   24 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7283 (tp40)
REVERT: C   34 LEU cc_start: 0.9456 (tp) cc_final: 0.8865 (tp)
REVERT: C   41 GLU cc_start: 0.8489 (pm20) cc_final: 0.8082 (mp0)
REVERT: C   43 VAL cc_start: 0.9487 (t) cc_final: 0.9203 (t)
REVERT: C   56 GLU cc_start: 0.7966 (tt0) cc_final: 0.7565 (tt0)
REVERT: C   87 ILE cc_start: 0.9622 (mm) cc_final: 0.9390 (mt)
REVERT: D   40 TYR cc_start: 0.8535 (m-80) cc_final: 0.8143 (m-80)
REVERT: D   57 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8717 (mptt)
REVERT: D   67 ASN cc_start: 0.8839 (m-40) cc_final: 0.8319 (t0)
REVERT: D   71 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: D   85 LYS cc_start: 0.8818 (mttt) cc_final: 0.8516 (mmtt)
REVERT: D  108 LYS cc_start: 0.9192 (tttt) cc_final: 0.8862 (ttpp)
REVERT: D  121 TYR cc_start: 0.9066 (t80) cc_final: 0.8786 (t80)
REVERT: E  111 TYR cc_start: 0.9414 (t80) cc_final: 0.9166 (t80)
REVERT: E  123 TYR cc_start: 0.8877 (m-80) cc_final: 0.8388 (m-10)
REVERT: E  139 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7829 (mt-10)
REVERT: F   27 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7909 (mm-40)
REVERT: F   51 TYR cc_start: 0.8384 (m-80) cc_final: 0.8125 (m-10)
REVERT: F   68 ASP cc_start: 0.8254 (m-30) cc_final: 0.7860 (m-30)
REVERT: F   98 TYR cc_start: 0.9104 (m-10) cc_final: 0.8759 (m-80)
REVERT: G   38 ASN cc_start: 0.8433 (t0) cc_final: 0.7805 (p0)
REVERT: G   75 LYS cc_start: 0.8402 (mmmm) cc_final: 0.7945 (mtpp)
REVERT: G   95 LYS cc_start: 0.8492 (tttm) cc_final: 0.8010 (mtpp)
REVERT: H   46 LYS cc_start: 0.9064 (mmpt) cc_final: 0.8200 (mmmt)
REVERT: H   57 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8805 (mptt)
REVERT: H   59 MET cc_start: 0.8802 (tpp) cc_final: 0.8520 (tpp)
REVERT: H   95 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8512 (tp40)
REVERT: M   50 HIS cc_start: 0.8968 (m-70) cc_final: 0.8059 (m-70)
REVERT: M   79 ASN cc_start: 0.8541 (m-40) cc_final: 0.7814 (t0)
REVERT: M  183 ASN cc_start: 0.7987 (m110) cc_final: 0.7503 (p0)
REVERT: M  188 HIS cc_start: 0.6754 (m-70) cc_final: 0.6081 (m170)
REVERT: M  190 MET cc_start: 0.7180 (tpp) cc_final: 0.6534 (tpp)
REVERT: N  195 HIS cc_start: 0.7703 (p-80) cc_final: 0.7444 (p-80)
  outliers start: 2
  outliers final: 0
  residues processed: 317
  average time/residue: 0.1450
  time to fit residues: 65.6944
Evaluate side-chains
  241 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 73 optimal weight:   30.0000
   chunk 102 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 119 optimal weight:    0.1980
   chunk 108 optimal weight:    9.9990
   chunk 93 optimal weight:   30.0000
   chunk 131 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.8388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
G  73 ASN
M 128 ASN
N  35 GLN
N  40 ASN
N  50 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.075634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.057175 restraints weight = 53826.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.057704 restraints weight = 40284.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.057931 restraints weight = 34692.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.058145 restraints weight = 29001.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.058202 restraints weight = 26172.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  16588  Z= 0.173
  Angle     :  0.715   7.468  23646  Z= 0.400
  Chirality :  0.050   0.227   2659
  Planarity :  0.005   0.063   1979
  Dihedral  : 32.254 115.004   4522
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.23), residues: 1171
  helix: -0.64 (0.19), residues: 669
  sheet: -0.41 (0.53), residues: 84
  loop : -2.16 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  92 
 TYR   0.022   0.002   TYR G  57 
 PHE   0.015   0.002   PHE N 100 
 TRP   0.015   0.001   TRP K 668 
 HIS   0.011   0.002   HIS N  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.17 (16588)
  covalent geometry    : angle       0.71490 /  0.40 (23646)
  hydrogen bonds       : bond        0.05453 /  3.65 (  837)
  hydrogen bonds       : angle       3.84426 /  2.67 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 291
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8304 (tt0) cc_final: 0.8054 (tt0)
REVERT: A  137 GLN cc_start: 0.7989 (mm110) cc_final: 0.7684 (mp10)
REVERT: B   59 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8509 (tppt)
REVERT: B   63 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8227 (mt-10)
REVERT: B   68 ASP cc_start: 0.8326 (m-30) cc_final: 0.8108 (m-30)
REVERT: B   88 TYR cc_start: 0.7856 (m-10) cc_final: 0.7092 (m-10)
REVERT: C   24 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7567 (tp40)
REVERT: C   41 GLU cc_start: 0.8418 (pm20) cc_final: 0.8192 (mp0)
REVERT: C   56 GLU cc_start: 0.7915 (tt0) cc_final: 0.7562 (tt0)
REVERT: C   87 ILE cc_start: 0.9634 (mm) cc_final: 0.9398 (mt)
REVERT: D   57 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8788 (mptt)
REVERT: D   67 ASN cc_start: 0.8964 (m-40) cc_final: 0.8390 (t0)
REVERT: D   71 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7870 (tm-30)
REVERT: D   85 LYS cc_start: 0.8860 (mttt) cc_final: 0.8550 (mmtt)
REVERT: D  108 LYS cc_start: 0.9278 (tttt) cc_final: 0.8946 (ttpp)
REVERT: D  121 TYR cc_start: 0.9047 (t80) cc_final: 0.8762 (t80)
REVERT: E   96 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8994 (tp40)
REVERT: E   97 GLU cc_start: 0.8673 (tp30) cc_final: 0.8195 (mm-30)
REVERT: E  111 TYR cc_start: 0.9461 (t80) cc_final: 0.9199 (t80)
REVERT: E  123 TYR cc_start: 0.8804 (m-80) cc_final: 0.8588 (m-10)
REVERT: E  137 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8109 (mm-40)
REVERT: E  139 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7362 (mt-10)
REVERT: F   51 TYR cc_start: 0.8253 (m-80) cc_final: 0.8018 (m-10)
REVERT: F   59 LYS cc_start: 0.8721 (ttmt) cc_final: 0.7965 (ttpt)
REVERT: F   61 PHE cc_start: 0.9289 (t80) cc_final: 0.9023 (t80)
REVERT: F   95 ARG cc_start: 0.8654 (ptp-110) cc_final: 0.8209 (ttp-110)
REVERT: G   38 ASN cc_start: 0.8251 (t0) cc_final: 0.7868 (p0)
REVERT: G   57 TYR cc_start: 0.8680 (t80) cc_final: 0.8448 (t80)
REVERT: G   75 LYS cc_start: 0.8458 (mmmm) cc_final: 0.7980 (mtpp)
REVERT: G   95 LYS cc_start: 0.8577 (tttm) cc_final: 0.7989 (ttmm)
REVERT: H   46 LYS cc_start: 0.8995 (mmpt) cc_final: 0.8639 (mmmt)
REVERT: H   71 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7845 (tm-30)
REVERT: H   95 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8594 (tp40)
REVERT: H  121 TYR cc_start: 0.9074 (t80) cc_final: 0.8748 (t80)
REVERT: L  656 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7220 (tpp80)
REVERT: M    3 GLU cc_start: 0.7637 (mp0) cc_final: 0.7089 (pm20)
REVERT: M   33 GLU cc_start: 0.6946 (tm-30) cc_final: 0.5744 (tm-30)
REVERT: M   50 HIS cc_start: 0.8961 (m-70) cc_final: 0.8169 (m-70)
REVERT: M   57 GLU cc_start: 0.8225 (pt0) cc_final: 0.7893 (pp20)
REVERT: M   79 ASN cc_start: 0.8493 (m-40) cc_final: 0.7805 (t0)
REVERT: M  183 ASN cc_start: 0.7836 (m110) cc_final: 0.7445 (p0)
REVERT: M  190 MET cc_start: 0.7215 (tpp) cc_final: 0.6706 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1436
  time to fit residues: 59.4674
Evaluate side-chains
  222 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 99 optimal weight:   40.0000
   chunk 58 optimal weight:    4.9990
   chunk 79 optimal weight:   30.0000
   chunk 27 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9990
   chunk 92 optimal weight:   20.0000
   chunk 129 optimal weight:   10.0000
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
** D  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
M 121 ASN
M 128 ASN
** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 188 HIS
N  50 HIS
N  75 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.076395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.058033 restraints weight = 52725.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.058214 restraints weight = 38788.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.058495 restraints weight = 34641.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.058699 restraints weight = 30235.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.058786 restraints weight = 27291.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16588  Z= 0.149
  Angle     :  0.674   7.100  23646  Z= 0.378
  Chirality :  0.048   0.229   2659
  Planarity :  0.005   0.048   1979
  Dihedral  : 32.014 113.082   4522
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  2.70 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.24), residues: 1171
  helix: -0.29 (0.20), residues: 666
  sheet: -0.58 (0.54), residues: 88
  loop : -1.99 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.019   0.001   TYR H  40 
 PHE   0.015   0.001   PHE N 205 
 TRP   0.011   0.001   TRP N 136 
 HIS   0.014   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.15 (16588)
  covalent geometry    : angle       0.67381 /  0.38 (23646)
  hydrogen bonds       : bond        0.05000 /  3.32 (  837)
  hydrogen bonds       : angle       3.61150 /  2.52 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 295
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 GLN cc_start: 0.8063 (mm110) cc_final: 0.7689 (mp10)
REVERT: B   59 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8045 (ttpt)
REVERT: B   63 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8039 (mt-10)
REVERT: B   68 ASP cc_start: 0.8250 (m-30) cc_final: 0.8011 (m-30)
REVERT: B   88 TYR cc_start: 0.7689 (m-10) cc_final: 0.7148 (m-10)
REVERT: C   24 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7704 (tp40)
REVERT: C   41 GLU cc_start: 0.8506 (pm20) cc_final: 0.8297 (mp0)
REVERT: C   56 GLU cc_start: 0.7803 (tt0) cc_final: 0.7496 (tt0)
REVERT: C   61 GLU cc_start: 0.8568 (tp30) cc_final: 0.8136 (tp30)
REVERT: C   87 ILE cc_start: 0.9617 (mm) cc_final: 0.9405 (mt)
REVERT: D   57 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8617 (mptt)
REVERT: D   67 ASN cc_start: 0.9036 (m-40) cc_final: 0.8505 (t0)
REVERT: D   71 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: D   85 LYS cc_start: 0.8878 (mttt) cc_final: 0.8549 (mmtt)
REVERT: D  108 LYS cc_start: 0.9247 (tttt) cc_final: 0.8943 (ttpp)
REVERT: D  121 TYR cc_start: 0.9047 (t80) cc_final: 0.8771 (t80)
REVERT: E   96 GLN cc_start: 0.9392 (tp-100) cc_final: 0.9181 (tp40)
REVERT: E  137 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8162 (mm-40)
REVERT: E  139 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7589 (mt-10)
REVERT: F   31 LYS cc_start: 0.8780 (tppt) cc_final: 0.8343 (tppp)
REVERT: F   59 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8092 (ttpt)
REVERT: F   98 TYR cc_start: 0.9112 (m-10) cc_final: 0.8867 (m-10)
REVERT: G   36 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8841 (mmmm)
REVERT: G   38 ASN cc_start: 0.8292 (t0) cc_final: 0.7878 (p0)
REVERT: G   57 TYR cc_start: 0.8841 (t80) cc_final: 0.8625 (t80)
REVERT: G   95 LYS cc_start: 0.8578 (tttm) cc_final: 0.7975 (ttmm)
REVERT: H   95 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8589 (tp40)
REVERT: H  121 TYR cc_start: 0.9145 (t80) cc_final: 0.8788 (t80)
REVERT: K  665 LEU cc_start: 0.8373 (tt) cc_final: 0.7333 (tt)
REVERT: L  656 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.7370 (tpp80)
REVERT: M   50 HIS cc_start: 0.8935 (m-70) cc_final: 0.8138 (m-70)
REVERT: M   57 GLU cc_start: 0.8268 (pt0) cc_final: 0.7936 (pp20)
REVERT: M   58 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6747 (mm-30)
REVERT: M   79 ASN cc_start: 0.8460 (m-40) cc_final: 0.7880 (t0)
REVERT: M  188 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6401 (m-70)
REVERT: M  190 MET cc_start: 0.6953 (tpp) cc_final: 0.6467 (tpp)
  outliers start: 5
  outliers final: 1
  residues processed: 297
  average time/residue: 0.1372
  time to fit residues: 59.1874
Evaluate side-chains
  225 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 223
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:   40.0000
   chunk 32 optimal weight:    0.8980
   chunk 126 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 133 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
D  84 ASN
H 109 HIS
M  37 GLN
M 128 ASN
N  35 GLN
N  50 HIS
N  74 ASN
N 128 ASN
N 156 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.076664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.058587 restraints weight = 52400.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.059042 restraints weight = 37998.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.059341 restraints weight = 32946.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.059542 restraints weight = 27211.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.059618 restraints weight = 24756.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  16588  Z= 0.137
  Angle     :  0.659   7.394  23646  Z= 0.371
  Chirality :  0.047   0.210   2659
  Planarity :  0.005   0.059   1979
  Dihedral  : 31.817 111.262   4522
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.24), residues: 1171
  helix: -0.03 (0.20), residues: 660
  sheet: -0.44 (0.54), residues: 88
  loop : -1.86 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K 659 
 TYR   0.012   0.001   TYR A 111 
 PHE   0.008   0.001   PHE A  79 
 TRP   0.008   0.001   TRP L 668 
 HIS   0.009   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.14 (16588)
  covalent geometry    : angle       0.65893 /  0.37 (23646)
  hydrogen bonds       : bond        0.04743 /  3.16 (  837)
  hydrogen bonds       : angle       3.46169 /  2.42 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9167 (mm) cc_final: 0.8731 (mt)
REVERT: A  137 GLN cc_start: 0.8033 (mm110) cc_final: 0.7707 (mp10)
REVERT: B   59 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8497 (ttpt)
REVERT: B   68 ASP cc_start: 0.8335 (m-30) cc_final: 0.7814 (m-30)
REVERT: B   85 ASP cc_start: 0.8548 (m-30) cc_final: 0.8315 (m-30)
REVERT: C   24 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7658 (tp40)
REVERT: C   56 GLU cc_start: 0.7913 (tt0) cc_final: 0.7566 (tt0)
REVERT: C   61 GLU cc_start: 0.8604 (tp30) cc_final: 0.8187 (tp30)
REVERT: D   57 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8562 (mptt)
REVERT: D   62 MET cc_start: 0.9290 (tpp) cc_final: 0.8873 (tpp)
REVERT: D   67 ASN cc_start: 0.8992 (m-40) cc_final: 0.8497 (t0)
REVERT: D   71 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: D   83 TYR cc_start: 0.8359 (m-10) cc_final: 0.8133 (m-10)
REVERT: D   85 LYS cc_start: 0.8862 (mttt) cc_final: 0.8496 (mmtt)
REVERT: D  108 LYS cc_start: 0.9246 (tttt) cc_final: 0.8942 (ttpp)
REVERT: D  121 TYR cc_start: 0.9035 (t80) cc_final: 0.8775 (t80)
REVERT: E   97 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8274 (mm-30)
REVERT: E  137 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8137 (mm-40)
REVERT: E  139 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7469 (mt-10)
REVERT: F   59 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7972 (ttpt)
REVERT: F   98 TYR cc_start: 0.9091 (m-10) cc_final: 0.8826 (m-10)
REVERT: G   36 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8810 (mmmm)
REVERT: G   38 ASN cc_start: 0.8186 (t0) cc_final: 0.7856 (p0)
REVERT: G   40 SER cc_start: 0.9328 (t) cc_final: 0.9091 (t)
REVERT: G   57 TYR cc_start: 0.8804 (t80) cc_final: 0.8569 (t80)
REVERT: G   95 LYS cc_start: 0.8284 (tttm) cc_final: 0.7950 (ttmm)
REVERT: H   46 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8300 (mmmt)
REVERT: H   95 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8524 (tp40)
REVERT: H  105 GLU cc_start: 0.8295 (pm20) cc_final: 0.7962 (pt0)
REVERT: M   50 HIS cc_start: 0.8999 (m-70) cc_final: 0.8283 (m-70)
REVERT: M   57 GLU cc_start: 0.8274 (pt0) cc_final: 0.7933 (pp20)
REVERT: M   58 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6744 (mm-30)
REVERT: M   79 ASN cc_start: 0.8501 (m-40) cc_final: 0.7918 (t0)
REVERT: N   46 GLU cc_start: 0.8747 (pp20) cc_final: 0.8365 (pp20)
REVERT: N   56 CYS cc_start: 0.8141 (m) cc_final: 0.7842 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1323
  time to fit residues: 54.8764
Evaluate side-chains
  216 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 93 optimal weight:   30.0000
   chunk 72 optimal weight:   30.0000
   chunk 106 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 120 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 129 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
D  84 ASN
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS
M 188 HIS
N  35 GLN
** N 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.076553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.058159 restraints weight = 52240.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.058658 restraints weight = 38281.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.058931 restraints weight = 32967.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.059145 restraints weight = 27532.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.059205 restraints weight = 25058.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16588  Z= 0.142
  Angle     :  0.658   7.358  23646  Z= 0.368
  Chirality :  0.047   0.205   2659
  Planarity :  0.005   0.052   1979
  Dihedral  : 31.693 109.658   4522
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.28 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.24), residues: 1171
  helix:  0.06 (0.20), residues: 663
  sheet: -0.24 (0.54), residues: 88
  loop : -1.70 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  86 
 TYR   0.019   0.001   TYR H 121 
 PHE   0.016   0.001   PHE N 205 
 TRP   0.008   0.001   TRP K 668 
 HIS   0.013   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.14 (16588)
  covalent geometry    : angle       0.65809 /  0.37 (23646)
  hydrogen bonds       : bond        0.04665 /  3.09 (  837)
  hydrogen bonds       : angle       3.39183 /  2.36 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 277
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 GLN cc_start: 0.7620 (mm110) cc_final: 0.7206 (mp10)
REVERT: B   24 ASP cc_start: 0.6655 (m-30) cc_final: 0.6431 (t0)
REVERT: B   59 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8398 (ttmt)
REVERT: B   63 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7877 (mt-10)
REVERT: B   68 ASP cc_start: 0.8189 (m-30) cc_final: 0.7817 (m-30)
REVERT: C   24 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7674 (tp40)
REVERT: C   56 GLU cc_start: 0.7883 (tt0) cc_final: 0.7580 (tt0)
REVERT: C   92 GLU cc_start: 0.7958 (tt0) cc_final: 0.7592 (tm-30)
REVERT: D   57 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8600 (mptt)
REVERT: D   62 MET cc_start: 0.9278 (tpp) cc_final: 0.8846 (tpp)
REVERT: D   67 ASN cc_start: 0.8956 (m-40) cc_final: 0.8484 (t0)
REVERT: D   71 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: D   76 GLU cc_start: 0.8968 (tp30) cc_final: 0.8733 (mm-30)
REVERT: D   83 TYR cc_start: 0.8381 (m-10) cc_final: 0.8039 (m-10)
REVERT: D   85 LYS cc_start: 0.8852 (mttt) cc_final: 0.8542 (mmtt)
REVERT: D  100 LEU cc_start: 0.9079 (tp) cc_final: 0.8368 (tp)
REVERT: D  108 LYS cc_start: 0.9236 (tttt) cc_final: 0.9022 (ttpp)
REVERT: D  121 TYR cc_start: 0.9040 (t80) cc_final: 0.8780 (t80)
REVERT: E   97 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8181 (mm-30)
REVERT: E  137 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7561 (mm-40)
REVERT: E  139 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7387 (mt-10)
REVERT: F   98 TYR cc_start: 0.9083 (m-10) cc_final: 0.8856 (m-10)
REVERT: G   95 LYS cc_start: 0.8281 (tttm) cc_final: 0.7956 (ttmm)
REVERT: G   99 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7963 (mtp180)
REVERT: H   46 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8279 (mmmt)
REVERT: M   40 ASN cc_start: 0.8601 (t0) cc_final: 0.8368 (t0)
REVERT: M   50 HIS cc_start: 0.8971 (m-70) cc_final: 0.8318 (m-70)
REVERT: M   57 GLU cc_start: 0.8273 (pt0) cc_final: 0.7901 (pp20)
REVERT: M   58 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6684 (mm-30)
REVERT: M   79 ASN cc_start: 0.8506 (m-40) cc_final: 0.7922 (t0)
REVERT: N   46 GLU cc_start: 0.8826 (pp20) cc_final: 0.8416 (pp20)
REVERT: N   56 CYS cc_start: 0.8045 (m) cc_final: 0.7794 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 277
  average time/residue: 0.1397
  time to fit residues: 55.6741
Evaluate side-chains
  219 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 89 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0770
   chunk 80 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 120 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.8144

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS
** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 GLN
N 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.075885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.057965 restraints weight = 51846.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.058421 restraints weight = 37980.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.058681 restraints weight = 32654.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.058902 restraints weight = 27154.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.058969 restraints weight = 24696.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  16588  Z= 0.158
  Angle     :  0.673   9.200  23646  Z= 0.371
  Chirality :  0.047   0.238   2659
  Planarity :  0.005   0.050   1979
  Dihedral  : 31.645 108.720   4522
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.24), residues: 1171
  helix:  0.13 (0.20), residues: 660
  sheet: -0.38 (0.54), residues: 92
  loop : -1.59 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  86 
 TYR   0.020   0.001   TYR H  83 
 PHE   0.012   0.001   PHE E  79 
 TRP   0.008   0.001   TRP K 668 
 HIS   0.007   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.16 (16588)
  covalent geometry    : angle       0.67311 /  0.37 (23646)
  hydrogen bonds       : bond        0.04720 /  3.13 (  837)
  hydrogen bonds       : angle       3.38893 /  2.36 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8293 (tt0) cc_final: 0.8035 (tt0)
REVERT: A   92 LEU cc_start: 0.9251 (mm) cc_final: 0.8818 (mt)
REVERT: B   24 ASP cc_start: 0.6815 (m-30) cc_final: 0.6511 (t0)
REVERT: B   68 ASP cc_start: 0.8204 (m-30) cc_final: 0.7798 (m-30)
REVERT: B   88 TYR cc_start: 0.7779 (m-10) cc_final: 0.7253 (m-10)
REVERT: C   24 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7758 (tp40)
REVERT: C   41 GLU cc_start: 0.8691 (pm20) cc_final: 0.8145 (mp0)
REVERT: C   56 GLU cc_start: 0.7910 (tt0) cc_final: 0.7647 (tt0)
REVERT: C   92 GLU cc_start: 0.8404 (tt0) cc_final: 0.7703 (tp30)
REVERT: D   57 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8562 (mptt)
REVERT: D   62 MET cc_start: 0.9271 (tpp) cc_final: 0.8848 (tpp)
REVERT: D   71 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: D   76 GLU cc_start: 0.8949 (tp30) cc_final: 0.8670 (mm-30)
REVERT: D   85 LYS cc_start: 0.8887 (mttt) cc_final: 0.8571 (mmtt)
REVERT: D  100 LEU cc_start: 0.9111 (tp) cc_final: 0.8345 (tp)
REVERT: D  108 LYS cc_start: 0.9241 (tttt) cc_final: 0.8951 (ttpp)
REVERT: D  121 TYR cc_start: 0.9048 (t80) cc_final: 0.8810 (t80)
REVERT: E   97 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8227 (mm-30)
REVERT: E  137 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7696 (mm-40)
REVERT: E  139 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7441 (mt-10)
REVERT: G   40 SER cc_start: 0.9265 (t) cc_final: 0.9054 (t)
REVERT: G   95 LYS cc_start: 0.8305 (tttm) cc_final: 0.8002 (ttmm)
REVERT: H   46 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8290 (mmmt)
REVERT: H   71 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: H   95 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8058 (tp40)
REVERT: M   50 HIS cc_start: 0.8994 (m-70) cc_final: 0.8445 (m-70)
REVERT: M   56 CYS cc_start: 0.7911 (m) cc_final: 0.7671 (m)
REVERT: M   57 GLU cc_start: 0.8305 (pt0) cc_final: 0.7916 (pp20)
REVERT: M   58 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6948 (mm-30)
REVERT: M   79 ASN cc_start: 0.8503 (m-40) cc_final: 0.7910 (t0)
REVERT: N   46 GLU cc_start: 0.8782 (pp20) cc_final: 0.8405 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.1266
  time to fit residues: 50.1924
Evaluate side-chains
  214 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 120 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 80 optimal weight:   30.0000
   chunk 72 optimal weight:   30.0000
   chunk 117 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 85 optimal weight:   40.0000
   chunk 94 optimal weight:   30.0000
   chunk 87 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 51 optimal weight:    0.7980
   overall best weight:    4.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  67 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 128 ASN
M 144 ASN
M 188 HIS
N  35 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.073571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.054989 restraints weight = 53156.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.055180 restraints weight = 39717.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.055318 restraints weight = 35388.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.055659 restraints weight = 31146.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.055697 restraints weight = 28222.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  16588  Z= 0.288
  Angle     :  0.791   8.715  23646  Z= 0.425
  Chirality :  0.052   0.271   2659
  Planarity :  0.006   0.052   1979
  Dihedral  : 31.720 109.629   4522
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  1.74 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.24), residues: 1171
  helix: -0.12 (0.20), residues: 663
  sheet: -0.15 (0.55), residues: 88
  loop : -1.64 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  33 
 TYR   0.021   0.002   TYR A  85 
 PHE   0.018   0.002   PHE E  79 
 TRP   0.011   0.002   TRP A  87 
 HIS   0.009   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00615 /  0.29 (16588)
  covalent geometry    : angle       0.79063 /  0.42 (23646)
  hydrogen bonds       : bond        0.05800 /  3.83 (  837)
  hydrogen bonds       : angle       3.78210 /  2.65 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 249
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8285 (tt0) cc_final: 0.7993 (tt0)
REVERT: B   24 ASP cc_start: 0.6827 (m-30) cc_final: 0.6509 (t0)
REVERT: B   88 TYR cc_start: 0.7897 (m-10) cc_final: 0.7399 (m-10)
REVERT: C   24 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7715 (tp-100)
REVERT: C   41 GLU cc_start: 0.8715 (pm20) cc_final: 0.8193 (mp0)
REVERT: C   56 GLU cc_start: 0.7980 (tt0) cc_final: 0.7764 (tt0)
REVERT: D   71 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: D   76 GLU cc_start: 0.9052 (tp30) cc_final: 0.8744 (mm-30)
REVERT: D   85 LYS cc_start: 0.8988 (mttt) cc_final: 0.8631 (mmtt)
REVERT: D  100 LEU cc_start: 0.9162 (tp) cc_final: 0.8892 (tt)
REVERT: D  108 LYS cc_start: 0.9271 (tttt) cc_final: 0.9010 (ttpp)
REVERT: D  121 TYR cc_start: 0.9102 (t80) cc_final: 0.8850 (t80)
REVERT: E   97 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8396 (mm-30)
REVERT: E  137 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8021 (mm-40)
REVERT: E  139 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7862 (mt-10)
REVERT: F   85 ASP cc_start: 0.8233 (m-30) cc_final: 0.7899 (m-30)
REVERT: G   40 SER cc_start: 0.9404 (t) cc_final: 0.9159 (t)
REVERT: G   95 LYS cc_start: 0.8503 (tttm) cc_final: 0.8200 (ttmm)
REVERT: G  104 GLN cc_start: 0.8722 (mt0) cc_final: 0.8285 (mt0)
REVERT: H   46 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8361 (mmmt)
REVERT: H   71 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: K  665 LEU cc_start: 0.8644 (tt) cc_final: 0.8410 (tt)
REVERT: M   50 HIS cc_start: 0.8996 (m-70) cc_final: 0.8585 (m-70)
REVERT: M   57 GLU cc_start: 0.8360 (pt0) cc_final: 0.7954 (pp20)
REVERT: M   58 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6875 (mm-30)
REVERT: M   79 ASN cc_start: 0.8533 (m-40) cc_final: 0.7912 (t0)
REVERT: M  188 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6715 (m-70)
REVERT: N   46 GLU cc_start: 0.8802 (pp20) cc_final: 0.8488 (pp20)
REVERT: N   71 ILE cc_start: 0.9284 (pt) cc_final: 0.9038 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1279
  time to fit residues: 46.5649
Evaluate side-chains
  208 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.1980
   chunk 86 optimal weight:   30.0000
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 137 optimal weight:    7.9990
   chunk 134 optimal weight:    7.9990
   chunk 95 optimal weight:   30.0000
   chunk 23 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 128 ASN
N  35 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.075744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.057075 restraints weight = 52651.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.057460 restraints weight = 39567.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.057751 restraints weight = 34684.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.057931 restraints weight = 28705.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.058005 restraints weight = 26210.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  16588  Z= 0.153
  Angle     :  0.690   9.881  23646  Z= 0.380
  Chirality :  0.048   0.273   2659
  Planarity :  0.005   0.047   1979
  Dihedral  : 31.638 108.431   4522
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.97 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.24), residues: 1171
  helix:  0.17 (0.20), residues: 669
  sheet: -0.08 (0.55), residues: 88
  loop : -1.54 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  86 
 TYR   0.015   0.001   TYR E 111 
 PHE   0.012   0.001   PHE E  79 
 TRP   0.017   0.001   TRP A  87 
 HIS   0.009   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.15 (16588)
  covalent geometry    : angle       0.69030 /  0.38 (23646)
  hydrogen bonds       : bond        0.04954 /  3.28 (  837)
  hydrogen bonds       : angle       3.49144 /  2.44 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 268
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8229 (tt0) cc_final: 0.7962 (tt0)
REVERT: B   24 ASP cc_start: 0.6795 (m-30) cc_final: 0.6575 (t0)
REVERT: B   88 TYR cc_start: 0.7830 (m-10) cc_final: 0.7348 (m-10)
REVERT: C   24 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7607 (tp-100)
REVERT: C   41 GLU cc_start: 0.8694 (pm20) cc_final: 0.8150 (mp0)
REVERT: C   56 GLU cc_start: 0.7907 (tt0) cc_final: 0.7610 (tt0)
REVERT: C   92 GLU cc_start: 0.8785 (tp30) cc_final: 0.8532 (tp30)
REVERT: D   62 MET cc_start: 0.9236 (tpp) cc_final: 0.8848 (tpp)
REVERT: D   71 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: D   76 GLU cc_start: 0.8808 (tp30) cc_final: 0.8608 (mm-30)
REVERT: D   85 LYS cc_start: 0.8945 (mttt) cc_final: 0.8626 (mmtt)
REVERT: D  108 LYS cc_start: 0.9253 (tttt) cc_final: 0.8954 (ttpp)
REVERT: D  120 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8852 (mtpt)
REVERT: D  121 TYR cc_start: 0.9025 (t80) cc_final: 0.8767 (t80)
REVERT: E   97 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8309 (mm-30)
REVERT: E  139 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7657 (mt-10)
REVERT: F   85 ASP cc_start: 0.8221 (m-30) cc_final: 0.7986 (m-30)
REVERT: G   40 SER cc_start: 0.9290 (t) cc_final: 0.9089 (t)
REVERT: G   95 LYS cc_start: 0.8315 (tttm) cc_final: 0.8062 (ttmm)
REVERT: H   46 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8387 (mmmt)
REVERT: H   71 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7673 (tm-30)
REVERT: M   56 CYS cc_start: 0.7883 (m) cc_final: 0.7637 (m)
REVERT: M   57 GLU cc_start: 0.8351 (pt0) cc_final: 0.7937 (pp20)
REVERT: M   58 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6858 (mm-30)
REVERT: M   79 ASN cc_start: 0.8474 (m-40) cc_final: 0.7904 (t0)
REVERT: N   46 GLU cc_start: 0.8749 (pp20) cc_final: 0.8449 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1258
  time to fit residues: 49.4231
Evaluate side-chains
  214 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 79 optimal weight:   30.0000
   chunk 66 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 30 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   chunk 126 optimal weight:    2.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  67 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  50 HIS
M 144 ASN
M 188 HIS
N  35 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.075693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.057127 restraints weight = 52337.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.057242 restraints weight = 39194.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.057517 restraints weight = 34678.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.057745 restraints weight = 30222.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.057805 restraints weight = 27721.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16588  Z= 0.163
  Angle     :  0.701   8.893  23646  Z= 0.383
  Chirality :  0.047   0.259   2659
  Planarity :  0.005   0.046   1979
  Dihedral  : 31.555 106.942   4522
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.29 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.24), residues: 1171
  helix:  0.24 (0.20), residues: 666
  sheet: -0.04 (0.55), residues: 88
  loop : -1.51 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  86 
 TYR   0.026   0.002   TYR F  88 
 PHE   0.019   0.002   PHE N 205 
 TRP   0.026   0.002   TRP L 668 
 HIS   0.011   0.001   HIS M  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.16 (16588)
  covalent geometry    : angle       0.70110 /  0.38 (23646)
  hydrogen bonds       : bond        0.04860 /  3.22 (  837)
  hydrogen bonds       : angle       3.50967 /  2.47 ( 2112)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 260
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.6826 (m-30) cc_final: 0.6544 (t0)
REVERT: B   88 TYR cc_start: 0.7816 (m-10) cc_final: 0.7329 (m-10)
REVERT: C   24 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7615 (tp-100)
REVERT: C   41 GLU cc_start: 0.8727 (pm20) cc_final: 0.8186 (mp0)
REVERT: C   56 GLU cc_start: 0.7910 (tt0) cc_final: 0.7651 (tt0)
REVERT: C   61 GLU cc_start: 0.8390 (tp30) cc_final: 0.8118 (tp30)
REVERT: D   71 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: D   85 LYS cc_start: 0.8964 (mttt) cc_final: 0.8613 (mmtt)
REVERT: D  108 LYS cc_start: 0.9272 (tttt) cc_final: 0.8961 (ttpp)
REVERT: D  120 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8866 (mtpt)
REVERT: D  121 TYR cc_start: 0.9112 (t80) cc_final: 0.8835 (t80)
REVERT: E   97 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8366 (mm-30)
REVERT: E  139 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7811 (mt-10)
REVERT: F   85 ASP cc_start: 0.8256 (m-30) cc_final: 0.7982 (m-30)
REVERT: F   98 TYR cc_start: 0.9112 (m-10) cc_final: 0.8834 (m-80)
REVERT: G   40 SER cc_start: 0.9261 (t) cc_final: 0.9031 (t)
REVERT: G   95 LYS cc_start: 0.8379 (tttm) cc_final: 0.8132 (ttmm)
REVERT: H   46 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8395 (mmmt)
REVERT: H   71 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: K  667 TYR cc_start: 0.8709 (p90) cc_final: 0.8381 (p90)
REVERT: M   56 CYS cc_start: 0.7866 (m) cc_final: 0.7620 (m)
REVERT: M   57 GLU cc_start: 0.8357 (pt0) cc_final: 0.7926 (pp20)
REVERT: M   58 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6848 (mm-30)
REVERT: M   79 ASN cc_start: 0.8521 (m-40) cc_final: 0.7898 (t0)
REVERT: N   46 GLU cc_start: 0.8710 (pp20) cc_final: 0.8402 (pp20)
REVERT: N   71 ILE cc_start: 0.9268 (pt) cc_final: 0.9040 (tp)
REVERT: N  119 THR cc_start: 0.9483 (m) cc_final: 0.9068 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1258
  time to fit residues: 48.1183
Evaluate side-chains
  211 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 75 optimal weight:   30.0000
   chunk 41 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 49 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.5784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  82 HIS
M 144 ASN
N  35 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.075514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.057389 restraints weight = 51966.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.057782 restraints weight = 38357.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.058090 restraints weight = 33035.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.058282 restraints weight = 27431.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.058363 restraints weight = 25135.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16588  Z= 0.151
  Angle     :  0.681   9.050  23646  Z= 0.374
  Chirality :  0.047   0.246   2659
  Planarity :  0.005   0.048   1979
  Dihedral  : 31.456 108.130   4522
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.77 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.25), residues: 1171
  helix:  0.37 (0.20), residues: 666
  sheet:  0.02 (0.55), residues: 88
  loop : -1.43 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  86 
 TYR   0.027   0.001   TYR F  88 
 PHE   0.012   0.001   PHE A  79 
 TRP   0.024   0.002   TRP L 668 
 HIS   0.008   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.15 (16588)
  covalent geometry    : angle       0.68104 /  0.37 (23646)
  hydrogen bonds       : bond        0.04774 /  3.16 (  837)
  hydrogen bonds       : angle       3.41375 /  2.38 ( 2112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2124.26 seconds
wall clock time: 37 minutes 40.99 seconds (2260.99 seconds total)