Starting phenix.real_space_refine
on Mon Apr  6 03:00:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bxt_30237/04_2026/7bxt_30237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bxt_30237/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bxt_30237/04_2026/7bxt_30237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bxt_30237/04_2026/7bxt_30237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bxt_30237/04_2026/7bxt_30237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bxt_30237/04_2026/7bxt_30237.cif"
  }
  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-2.1rc1-6017/lib/python3.9/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: 3.43, per 1000 atoms: 0.22
  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: 1.09
  Conformation dependent library (CDL) restraints added in 378.6 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: 2.32
  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: 2.47

  Time building geometry restraints manager: 1.55 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=" CB  TRP A  87 "
       pdb=" CG  TRP A  87 "
    ideal  model  delta    sigma   weight residual
    1.498  1.430  0.068 3.10e-02 1.04e+03 4.87e+00
  bond pdb=" CG  LEU C  83 "
       pdb=" CD2 LEU C  83 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.41e+00
  bond pdb=" CB  TRP M  83 "
       pdb=" CG  TRP M  83 "
    ideal  model  delta    sigma   weight residual
    1.498  1.441  0.057 3.10e-02 1.04e+03 3.33e+00
  bond pdb=" CB  TYR N 150 "
       pdb=" CG  TYR N 150 "
    ideal  model  delta    sigma   weight residual
    1.512  1.472  0.040 2.20e-02 2.07e+03 3.27e+00
  bond pdb=" CB  VAL B  81 "
       pdb=" CG2 VAL B  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.17e+00
  ... (remaining 16583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 23189
        2.67 -     5.33: 405
        5.33 -     8.00: 39
        8.00 -    10.67: 10
       10.67 -    13.33: 3
  Bond angle restraints: 23646
  Sorted by residual:
  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=" N   ARG K 655 "
        pdb=" CA  ARG K 655 "
        pdb=" C   ARG K 655 "
      ideal   model   delta    sigma   weight residual
     110.80  101.91    8.89 2.13e+00 2.20e-01 1.74e+01
  angle pdb=" N   VAL L 654 "
        pdb=" CA  VAL L 654 "
        pdb=" C   VAL L 654 "
      ideal   model   delta    sigma   weight residual
     113.47  109.40    4.07 1.01e+00 9.80e-01 1.63e+01
  angle pdb=" CA  LEU L 662 "
        pdb=" CB  LEU L 662 "
        pdb=" CG  LEU L 662 "
      ideal   model   delta    sigma   weight residual
     116.30  129.63  -13.33 3.50e+00 8.16e-02 1.45e+01
  angle pdb=" C   ASP N 127 "
        pdb=" N   ASN N 128 "
        pdb=" CA  ASN N 128 "
      ideal   model   delta    sigma   weight residual
     121.54  128.73   -7.19 1.91e+00 2.74e-01 1.42e+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: 2161
       0.067 -    0.133: 441
       0.133 -    0.200: 53
       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:             0.710
  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:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.080
  Find NCS groups from input model:        0.140
  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:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
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= 0.439
  Angle     :  0.942  13.331  23646  Z= 0.535
  Chirality :  0.053   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
  covalent geometry    : bond        0.00974 (16588)
  covalent geometry    : angle       0.94175 (23646)
  hydrogen bonds       : bond        0.14426 (  837)
  hydrogen bonds       : angle       5.98525 ( 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  : 0.442 
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: 0.7960 (mm-30)
REVERT: A   74 GLU cc_start: 0.8193 (tt0) cc_final: 0.7125 (tt0)
REVERT: A  105 HIS cc_start: 0.8107 (m-70) cc_final: 0.7810 (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: 0.7603 (tp40)
REVERT: C   34 LEU cc_start: 0.9483 (tp) cc_final: 0.8921 (tp)
REVERT: C   43 VAL cc_start: 0.9414 (t) cc_final: 0.9171 (t)
REVERT: C   87 ILE cc_start: 0.9714 (mm) cc_final: 0.9460 (mt)
REVERT: C   99 ARG cc_start: 0.7320 (ptt-90) cc_final: 0.6754 (ptp-170)
REVERT: D   57 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8768 (mptt)
REVERT: D   71 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: D   83 TYR cc_start: 0.8580 (m-10) cc_final: 0.8066 (m-10)
REVERT: D   85 LYS cc_start: 0.8783 (mttt) cc_final: 0.8551 (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  123 TYR cc_start: 0.8930 (m-80) cc_final: 0.8440 (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: 0.6050 (t0)
REVERT: G   38 ASN cc_start: 0.8572 (t0) cc_final: 0.8206 (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: 0.7698 (t0)
REVERT: H   57 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8778 (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: 0.8537 (tt)
REVERT: M    3 GLU cc_start: 0.8607 (mp0) cc_final: 0.8045 (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: 0.7953 (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: 0.8055 (t0)
REVERT: M  183 ASN cc_start: 0.8441 (m110) cc_final: 0.7818 (p0)
REVERT: M  191 GLU cc_start: 0.8269 (pm20) cc_final: 0.8046 (pm20)
REVERT: N   19 ASP cc_start: 0.8641 (m-30) cc_final: 0.8440 (m-30)
REVERT: N   22 MET cc_start: 0.8204 (mpp) cc_final: 0.8000 (mpp)
REVERT: N   30 PHE cc_start: 0.8448 (t80) cc_final: 0.8217 (t80)
REVERT: N  204 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8203 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 361
  average time/residue: 0.1521
  time to fit residues: 75.0992
Evaluate side-chains
  230 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 228
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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:    5.9990
   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:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 137 GLN
B  27 GLN
C  73 ASN
D  63 ASN
** D  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
E  40 HIS
E  96 GLN
G  73 ASN
G 110 ASN
H  63 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 112 GLN
M 128 ASN
M 144 ASN
M 188 HIS
N  35 GLN
N  74 ASN
N 128 ASN
N 170 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.076028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.057981 restraints weight = 52025.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.058543 restraints weight = 36136.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059002 restraints weight = 27519.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.059245 restraints weight = 25200.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.059327 restraints weight = 23301.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2834

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= 0.161
  Angle     :  0.643   8.650  23646  Z= 0.370
  Chirality :  0.040   0.194   2659
  Planarity :  0.005   0.069   1979
  Dihedral  : 32.042 114.820   4522
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.63 %
    Favored  : 95.17 %
  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: -2.20 (0.22), residues: 1171
  helix: -1.01 (0.18), residues: 664
  sheet: -0.86 (0.52), residues: 86
  loop : -2.16 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  86 
 TYR   0.013   0.001   TYR H  83 
 PHE   0.014   0.002   PHE M 122 
 TRP   0.020   0.001   TRP L 668 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (16588)
  covalent geometry    : angle       0.64291 (23646)
  hydrogen bonds       : bond        0.04454 (  837)
  hydrogen bonds       : angle       3.66996 ( 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
  327 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 325
  time to evaluate  : 0.476 
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: A   51 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7915 (mm-30)
REVERT: A   96 GLN cc_start: 0.9401 (tp40) cc_final: 0.9180 (mm-40)
REVERT: A  137 GLN cc_start: 0.7942 (mm110) cc_final: 0.7723 (mp10)
REVERT: B   30 THR cc_start: 0.9369 (t) cc_final: 0.9145 (m)
REVERT: C   24 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7549 (tp40)
REVERT: C   34 LEU cc_start: 0.9344 (tp) cc_final: 0.8810 (tp)
REVERT: C   43 VAL cc_start: 0.9565 (t) cc_final: 0.9302 (t)
REVERT: C   56 GLU cc_start: 0.8005 (tt0) cc_final: 0.7526 (tt0)
REVERT: D   57 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8780 (mptt)
REVERT: D   67 ASN cc_start: 0.9021 (m-40) cc_final: 0.8380 (t0)
REVERT: D   71 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: D   85 LYS cc_start: 0.8840 (mttt) cc_final: 0.8530 (mmtt)
REVERT: D  108 LYS cc_start: 0.9229 (tttt) cc_final: 0.8892 (ttpp)
REVERT: D  121 TYR cc_start: 0.9037 (t80) cc_final: 0.8786 (t80)
REVERT: E  108 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: F   58 LEU cc_start: 0.9515 (tp) cc_final: 0.9300 (tp)
REVERT: F   88 TYR cc_start: 0.7605 (m-10) cc_final: 0.7285 (m-10)
REVERT: F   98 TYR cc_start: 0.9166 (m-10) cc_final: 0.8528 (m-80)
REVERT: G   38 ASN cc_start: 0.8199 (t0) cc_final: 0.7923 (p0)
REVERT: G   57 TYR cc_start: 0.8696 (t80) cc_final: 0.8346 (t80)
REVERT: G   95 LYS cc_start: 0.8353 (tttm) cc_final: 0.7888 (ttmm)
REVERT: H   46 LYS cc_start: 0.9009 (mmpt) cc_final: 0.8330 (mmmt)
REVERT: H   57 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8788 (mptt)
REVERT: H   71 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: M   35 GLN cc_start: 0.8268 (mt0) cc_final: 0.7499 (mt0)
REVERT: M   46 GLU cc_start: 0.8372 (pp20) cc_final: 0.8083 (pp20)
REVERT: M   50 HIS cc_start: 0.9058 (m-70) cc_final: 0.8154 (m-70)
REVERT: M   79 ASN cc_start: 0.8439 (m-40) cc_final: 0.7825 (t0)
REVERT: M  183 ASN cc_start: 0.8092 (m110) cc_final: 0.7747 (p0)
REVERT: M  188 HIS cc_start: 0.6479 (m90) cc_final: 0.6043 (m170)
REVERT: N   87 HIS cc_start: 0.7693 (t70) cc_final: 0.7467 (t70)
REVERT: N  119 THR cc_start: 0.9495 (m) cc_final: 0.9050 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1344
  time to fit residues: 62.7586
Evaluate side-chains
  236 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9980
   chunk 119 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 93 optimal weight:    8.9990
   chunk 131 optimal weight:    0.0470
   chunk 18 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
E  96 GLN
G  73 ASN
H  49 HIS
H  84 ASN
N  35 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.077733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.058985 restraints weight = 53140.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.059374 restraints weight = 36795.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.059745 restraints weight = 29486.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.060017 restraints weight = 27566.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.060042 restraints weight = 24847.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16588  Z= 0.144
  Angle     :  0.606   8.822  23646  Z= 0.347
  Chirality :  0.038   0.209   2659
  Planarity :  0.005   0.056   1979
  Dihedral  : 31.449 113.631   4522
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.54 %
    Favored  : 95.37 %
  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: -1.30 (0.24), residues: 1171
  helix: -0.15 (0.20), residues: 662
  sheet: -0.68 (0.54), residues: 88
  loop : -1.94 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  92 
 TYR   0.018   0.001   TYR A 111 
 PHE   0.007   0.001   PHE N 122 
 TRP   0.012   0.001   TRP K 668 
 HIS   0.007   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (16588)
  covalent geometry    : angle       0.60641 (23646)
  hydrogen bonds       : bond        0.04138 (  837)
  hydrogen bonds       : angle       3.33793 ( 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
  302 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 301
  time to evaluate  : 0.412 
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: A  137 GLN cc_start: 0.8047 (mm110) cc_final: 0.7632 (mp10)
REVERT: B   24 ASP cc_start: 0.6799 (t0) cc_final: 0.6578 (t0)
REVERT: B   59 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8343 (ttpt)
REVERT: B   63 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8048 (mt-10)
REVERT: C   24 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7529 (tp40)
REVERT: C   34 LEU cc_start: 0.9375 (tp) cc_final: 0.9069 (tp)
REVERT: C   56 GLU cc_start: 0.7868 (tt0) cc_final: 0.7476 (tt0)
REVERT: C   79 ILE cc_start: 0.9333 (pt) cc_final: 0.8801 (mt)
REVERT: D   57 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8728 (mptt)
REVERT: D   67 ASN cc_start: 0.8982 (m-40) cc_final: 0.8429 (t0)
REVERT: D   71 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: D   85 LYS cc_start: 0.8933 (mttt) cc_final: 0.8591 (mmtt)
REVERT: D  108 LYS cc_start: 0.9209 (tttt) cc_final: 0.8948 (ttpp)
REVERT: D  121 TYR cc_start: 0.9024 (t80) cc_final: 0.8714 (t80)
REVERT: E   97 GLU cc_start: 0.8542 (tp30) cc_final: 0.8010 (mm-30)
REVERT: E  111 TYR cc_start: 0.9366 (t80) cc_final: 0.9093 (t80)
REVERT: E  137 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8187 (mm-40)
REVERT: F   59 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8314 (ttpt)
REVERT: F   88 TYR cc_start: 0.7466 (m-10) cc_final: 0.7208 (m-10)
REVERT: F   98 TYR cc_start: 0.9164 (m-10) cc_final: 0.8512 (m-80)
REVERT: G   38 ASN cc_start: 0.8205 (t0) cc_final: 0.7932 (t0)
REVERT: G   92 GLU cc_start: 0.7729 (pm20) cc_final: 0.7295 (pm20)
REVERT: G   95 LYS cc_start: 0.8404 (tttm) cc_final: 0.7816 (ttmm)
REVERT: H   46 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8392 (mmmt)
REVERT: K  660 ILE cc_start: 0.7837 (mm) cc_final: 0.7482 (mm)
REVERT: K  665 LEU cc_start: 0.8269 (tt) cc_final: 0.7167 (tt)
REVERT: M    3 GLU cc_start: 0.7852 (mp0) cc_final: 0.7331 (pm20)
REVERT: M   22 MET cc_start: 0.8536 (pmm) cc_final: 0.8273 (pmm)
REVERT: M   50 HIS cc_start: 0.8922 (m-70) cc_final: 0.8025 (m170)
REVERT: M   57 GLU cc_start: 0.8162 (pt0) cc_final: 0.7830 (pp20)
REVERT: M   58 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6659 (mm-30)
REVERT: M   79 ASN cc_start: 0.8446 (m-40) cc_final: 0.7903 (t0)
REVERT: M  178 MET cc_start: 0.7602 (ttt) cc_final: 0.7294 (tmm)
REVERT: N   22 MET cc_start: 0.8216 (mpp) cc_final: 0.7989 (mpp)
REVERT: N   46 GLU cc_start: 0.8916 (pp20) cc_final: 0.8497 (pp20)
REVERT: N   87 HIS cc_start: 0.7777 (t70) cc_final: 0.7454 (t70)
REVERT: N  178 MET cc_start: 0.7563 (ttp) cc_final: 0.7240 (ttp)
  outliers start: 1
  outliers final: 1
  residues processed: 302
  average time/residue: 0.1266
  time to fit residues: 55.7410
Evaluate side-chains
  240 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 132 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 129 optimal weight:    9.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 121 ASN
M 128 ASN
M 188 HIS
N  35 GLN
N  40 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.075994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.057126 restraints weight = 52673.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.057575 restraints weight = 38545.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.058146 restraints weight = 31623.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.058238 restraints weight = 26863.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.058257 restraints weight = 25409.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  16588  Z= 0.179
  Angle     :  0.614   7.339  23646  Z= 0.351
  Chirality :  0.038   0.139   2659
  Planarity :  0.004   0.054   1979
  Dihedral  : 31.367 114.082   4522
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.86 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.91 (0.24), residues: 1171
  helix:  0.13 (0.20), residues: 664
  sheet: -0.09 (0.55), residues: 82
  loop : -1.82 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.033   0.002   TYR D  83 
 PHE   0.013   0.001   PHE N 205 
 TRP   0.009   0.001   TRP K 668 
 HIS   0.006   0.001   HIS M 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (16588)
  covalent geometry    : angle       0.61381 (23646)
  hydrogen bonds       : bond        0.04306 (  837)
  hydrogen bonds       : angle       3.30652 ( 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
  287 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 285
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8336 (ttpt)
REVERT: B   63 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8018 (mt-10)
REVERT: B   85 ASP cc_start: 0.8439 (m-30) cc_final: 0.8199 (m-30)
REVERT: C   24 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7687 (tp40)
REVERT: C   34 LEU cc_start: 0.9311 (tp) cc_final: 0.9035 (tp)
REVERT: C   41 GLU cc_start: 0.8558 (pm20) cc_final: 0.8117 (mp0)
REVERT: C   56 GLU cc_start: 0.7903 (tt0) cc_final: 0.7510 (tt0)
REVERT: D   33 ARG cc_start: 0.8666 (tpp80) cc_final: 0.7856 (tpt170)
REVERT: D   57 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8744 (mptt)
REVERT: D   62 MET cc_start: 0.9065 (mmm) cc_final: 0.8343 (tpp)
REVERT: D   67 ASN cc_start: 0.9010 (m-40) cc_final: 0.8623 (t0)
REVERT: D   71 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: D   76 GLU cc_start: 0.8899 (tp30) cc_final: 0.8591 (mm-30)
REVERT: D   85 LYS cc_start: 0.8935 (mttt) cc_final: 0.8571 (mmtt)
REVERT: D  108 LYS cc_start: 0.9200 (tttt) cc_final: 0.8967 (ttpp)
REVERT: D  113 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8406 (mm-30)
REVERT: D  120 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8791 (mtpt)
REVERT: D  121 TYR cc_start: 0.9107 (t80) cc_final: 0.8816 (t80)
REVERT: E   97 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8390 (mm-30)
REVERT: E  111 TYR cc_start: 0.9420 (t80) cc_final: 0.9207 (t80)
REVERT: E  137 GLN cc_start: 0.8525 (mm-40) cc_final: 0.7435 (mm-40)
REVERT: E  139 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7831 (mt-10)
REVERT: F   98 TYR cc_start: 0.9134 (m-10) cc_final: 0.8849 (m-80)
REVERT: G   38 ASN cc_start: 0.8187 (t0) cc_final: 0.7701 (p0)
REVERT: G   40 SER cc_start: 0.9509 (t) cc_final: 0.9267 (t)
REVERT: G   57 TYR cc_start: 0.8806 (t80) cc_final: 0.8577 (t80)
REVERT: G   95 LYS cc_start: 0.8347 (tttm) cc_final: 0.8047 (ttmm)
REVERT: H   46 LYS cc_start: 0.8929 (mmpt) cc_final: 0.8453 (mmmt)
REVERT: H   71 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: H  120 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8804 (ptmm)
REVERT: K  660 ILE cc_start: 0.8362 (mm) cc_final: 0.8146 (mp)
REVERT: M   22 MET cc_start: 0.8587 (pmm) cc_final: 0.8353 (pmm)
REVERT: M   50 HIS cc_start: 0.8933 (m-70) cc_final: 0.8603 (m-70)
REVERT: M   56 CYS cc_start: 0.7952 (m) cc_final: 0.7676 (m)
REVERT: M   57 GLU cc_start: 0.8198 (pt0) cc_final: 0.7827 (pp20)
REVERT: M   58 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6494 (mm-30)
REVERT: M   79 ASN cc_start: 0.8500 (m-40) cc_final: 0.7949 (t0)
REVERT: M  188 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6635 (m-70)
REVERT: N   46 GLU cc_start: 0.8841 (pp20) cc_final: 0.8470 (pp20)
REVERT: N   56 CYS cc_start: 0.8089 (m) cc_final: 0.7830 (m)
REVERT: N   87 HIS cc_start: 0.7612 (t70) cc_final: 0.7223 (t70)
REVERT: N  119 THR cc_start: 0.9511 (m) cc_final: 0.9094 (p)
REVERT: N  122 PHE cc_start: 0.7334 (m-80) cc_final: 0.6589 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 286
  average time/residue: 0.1345
  time to fit residues: 55.6047
Evaluate side-chains
  234 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 232
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 126 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 133 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 124 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
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 = 0.3376 r_free = 0.3376 target = 0.075123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.056434 restraints weight = 52739.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.056897 restraints weight = 39247.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.057106 restraints weight = 33775.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.057308 restraints weight = 28776.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.057374 restraints weight = 25996.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
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      :  0.005   0.037  16588  Z= 0.219
  Angle     :  0.651   9.178  23646  Z= 0.367
  Chirality :  0.039   0.239   2659
  Planarity :  0.005   0.054   1979
  Dihedral  : 31.344 113.739   4522
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.03 %
    Favored  : 97.88 %
  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: -0.77 (0.24), residues: 1171
  helix:  0.16 (0.20), residues: 667
  sheet: -0.15 (0.57), residues: 86
  loop : -1.59 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  92 
 TYR   0.052   0.002   TYR D  83 
 PHE   0.012   0.001   PHE M 122 
 TRP   0.010   0.001   TRP K 668 
 HIS   0.006   0.001   HIS N  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (16588)
  covalent geometry    : angle       0.65095 (23646)
  hydrogen bonds       : bond        0.04573 (  837)
  hydrogen bonds       : angle       3.43952 ( 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
  280 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 279
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8456 (tt0) cc_final: 0.8151 (tt0)
REVERT: B   59 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8371 (ttmt)
REVERT: C   24 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7539 (tp40)
REVERT: C   34 LEU cc_start: 0.9382 (tp) cc_final: 0.9129 (tp)
REVERT: C   41 GLU cc_start: 0.8581 (pm20) cc_final: 0.8295 (mp0)
REVERT: C   56 GLU cc_start: 0.7908 (tt0) cc_final: 0.7520 (tt0)
REVERT: C   64 GLU cc_start: 0.5142 (tt0) cc_final: 0.4924 (tt0)
REVERT: D   57 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8774 (mptt)
REVERT: D   62 MET cc_start: 0.9189 (mmm) cc_final: 0.8398 (tpp)
REVERT: D   67 ASN cc_start: 0.9070 (m-40) cc_final: 0.8577 (t0)
REVERT: D   71 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7873 (tm-30)
REVERT: D   76 GLU cc_start: 0.8899 (tp30) cc_final: 0.8672 (mm-30)
REVERT: D   85 LYS cc_start: 0.9009 (mttt) cc_final: 0.8670 (mmtt)
REVERT: D  108 LYS cc_start: 0.9201 (tttt) cc_final: 0.8979 (ttpp)
REVERT: D  121 TYR cc_start: 0.9147 (t80) cc_final: 0.8868 (t80)
REVERT: E   97 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8465 (mm-30)
REVERT: E  137 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8258 (mm-40)
REVERT: E  139 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7702 (mt-10)
REVERT: F   85 ASP cc_start: 0.8148 (m-30) cc_final: 0.7845 (m-30)
REVERT: G   40 SER cc_start: 0.9482 (t) cc_final: 0.9268 (t)
REVERT: G   56 GLU cc_start: 0.7835 (pt0) cc_final: 0.7603 (tt0)
REVERT: G   62 ILE cc_start: 0.9605 (mt) cc_final: 0.9377 (tt)
REVERT: G   64 GLU cc_start: 0.7588 (tt0) cc_final: 0.7359 (tt0)
REVERT: G   95 LYS cc_start: 0.8553 (tttm) cc_final: 0.8237 (ttmm)
REVERT: H   46 LYS cc_start: 0.8881 (mmpt) cc_final: 0.8494 (mmmt)
REVERT: H   71 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: H   83 TYR cc_start: 0.8864 (m-10) cc_final: 0.8564 (m-10)
REVERT: H  120 LYS cc_start: 0.9192 (ptmm) cc_final: 0.8828 (ptmm)
REVERT: H  122 THR cc_start: 0.8802 (p) cc_final: 0.8548 (t)
REVERT: M   22 MET cc_start: 0.8603 (pmm) cc_final: 0.8364 (pmm)
REVERT: M   56 CYS cc_start: 0.7934 (m) cc_final: 0.7682 (m)
REVERT: M   57 GLU cc_start: 0.8115 (pt0) cc_final: 0.7844 (pp20)
REVERT: M   58 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6898 (mm-30)
REVERT: M   79 ASN cc_start: 0.8542 (m-40) cc_final: 0.7891 (t0)
REVERT: N   22 MET cc_start: 0.8085 (mpp) cc_final: 0.7852 (mpp)
REVERT: N   46 GLU cc_start: 0.8874 (pp20) cc_final: 0.8613 (pp20)
REVERT: N   87 HIS cc_start: 0.7601 (t70) cc_final: 0.7151 (t70)
REVERT: N  119 THR cc_start: 0.9501 (m) cc_final: 0.9086 (p)
REVERT: N  122 PHE cc_start: 0.7273 (m-80) cc_final: 0.6602 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 280
  average time/residue: 0.1356
  time to fit residues: 54.6601
Evaluate side-chains
  222 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 221
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 106 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 120 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 129 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
A 137 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  82 HIS
M 117 ASN
M 121 ASN
M 128 ASN
M 188 HIS
N  35 GLN
N  50 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.072117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.053359 restraints weight = 53527.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.053626 restraints weight = 40950.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.053853 restraints weight = 35276.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.054055 restraints weight = 30999.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.054115 restraints weight = 28273.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052  16588  Z= 0.340
  Angle     :  0.759   8.724  23646  Z= 0.423
  Chirality :  0.043   0.269   2659
  Planarity :  0.006   0.063   1979
  Dihedral  : 31.623 116.343   4522
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.15 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.15 (0.24), residues: 1171
  helix: -0.16 (0.19), residues: 675
  sheet: -0.37 (0.53), residues: 86
  loop : -1.73 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  86 
 TYR   0.047   0.003   TYR D  83 
 PHE   0.022   0.002   PHE E  79 
 TRP   0.041   0.003   TRP L 668 
 HIS   0.008   0.002   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00758 (16588)
  covalent geometry    : angle       0.75949 (23646)
  hydrogen bonds       : bond        0.05805 (  837)
  hydrogen bonds       : angle       3.99728 ( 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
  255 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8513 (tt0) cc_final: 0.8198 (tt0)
REVERT: B   25 ASN cc_start: 0.8034 (t0) cc_final: 0.7690 (t0)
REVERT: B   59 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8473 (ttpt)
REVERT: B   63 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8129 (mt-10)
REVERT: C   24 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7749 (tp-100)
REVERT: C   41 GLU cc_start: 0.8619 (pm20) cc_final: 0.8301 (mp0)
REVERT: C   56 GLU cc_start: 0.8003 (tt0) cc_final: 0.7636 (tt0)
REVERT: C   57 TYR cc_start: 0.9075 (t80) cc_final: 0.8464 (t80)
REVERT: D   62 MET cc_start: 0.9281 (mmm) cc_final: 0.8863 (tpp)
REVERT: D   67 ASN cc_start: 0.9126 (m-40) cc_final: 0.8665 (t0)
REVERT: D   85 LYS cc_start: 0.9067 (mttt) cc_final: 0.8670 (mmtt)
REVERT: D   86 ARG cc_start: 0.8816 (mpt-90) cc_final: 0.8445 (ttm-80)
REVERT: D   92 ARG cc_start: 0.8785 (ttt90) cc_final: 0.8521 (mtp85)
REVERT: D  121 TYR cc_start: 0.9223 (t80) cc_final: 0.8846 (t80)
REVERT: E   97 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8629 (mm-30)
REVERT: E  100 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8568 (mm-30)
REVERT: F   98 TYR cc_start: 0.9082 (m-80) cc_final: 0.8878 (m-80)
REVERT: G   95 LYS cc_start: 0.8754 (tttm) cc_final: 0.8245 (ttmm)
REVERT: H   71 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: H   83 TYR cc_start: 0.8947 (m-10) cc_final: 0.8698 (m-10)
REVERT: H  120 LYS cc_start: 0.9259 (ptmm) cc_final: 0.8901 (ptmm)
REVERT: M   22 MET cc_start: 0.8620 (pmm) cc_final: 0.8384 (pmm)
REVERT: M   57 GLU cc_start: 0.8228 (pt0) cc_final: 0.7951 (pp20)
REVERT: M   58 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6946 (mm-30)
REVERT: M   79 ASN cc_start: 0.8471 (m-40) cc_final: 0.8171 (m-40)
REVERT: M  196 CYS cc_start: 0.7356 (t) cc_final: 0.7105 (t)
REVERT: N   22 MET cc_start: 0.8085 (mpp) cc_final: 0.7846 (mpp)
REVERT: N   46 GLU cc_start: 0.8691 (pp20) cc_final: 0.8366 (pp20)
REVERT: N  119 THR cc_start: 0.9494 (m) cc_final: 0.9024 (p)
REVERT: N  122 PHE cc_start: 0.7475 (m-80) cc_final: 0.7046 (m-80)
REVERT: N  174 LEU cc_start: 0.9339 (tp) cc_final: 0.9113 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 254
  average time/residue: 0.1477
  time to fit residues: 52.9684
Evaluate side-chains
  197 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 89 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 120 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 110 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
** D  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
H  49 HIS
H  82 HIS
M  50 HIS
M 128 ASN
N  35 GLN
N  50 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.076109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.057167 restraints weight = 52027.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.057492 restraints weight = 38356.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.057903 restraints weight = 31690.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.058072 restraints weight = 28304.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.058100 restraints weight = 26401.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16588  Z= 0.154
  Angle     :  0.623  10.608  23646  Z= 0.355
  Chirality :  0.038   0.261   2659
  Planarity :  0.004   0.048   1979
  Dihedral  : 31.166 111.748   4522
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.90 %
    Favored  : 97.01 %
  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: -0.50 (0.24), residues: 1171
  helix:  0.44 (0.20), residues: 664
  sheet: -0.04 (0.58), residues: 74
  loop : -1.53 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  20 
 TYR   0.018   0.001   TYR B  51 
 PHE   0.015   0.001   PHE N 205 
 TRP   0.017   0.002   TRP A  87 
 HIS   0.009   0.001   HIS N  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (16588)
  covalent geometry    : angle       0.62262 (23646)
  hydrogen bonds       : bond        0.04263 (  837)
  hydrogen bonds       : angle       3.35472 ( 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
  275 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 274
  time to evaluate  : 0.432 
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: 0.8559 (tt0) cc_final: 0.8339 (tt0)
REVERT: B   31 LYS cc_start: 0.8499 (tppt) cc_final: 0.7984 (tppp)
REVERT: B   59 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8479 (ttpt)
REVERT: B   85 ASP cc_start: 0.8186 (m-30) cc_final: 0.7985 (m-30)
REVERT: C   24 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7646 (tp40)
REVERT: C   34 LEU cc_start: 0.9401 (tp) cc_final: 0.9196 (tp)
REVERT: C   41 GLU cc_start: 0.8494 (pm20) cc_final: 0.8167 (mp0)
REVERT: C   56 GLU cc_start: 0.7491 (tt0) cc_final: 0.7129 (tt0)
REVERT: D   62 MET cc_start: 0.9154 (mmm) cc_final: 0.8936 (tpp)
REVERT: D   67 ASN cc_start: 0.9066 (m-40) cc_final: 0.8603 (t0)
REVERT: D   83 TYR cc_start: 0.8221 (m-80) cc_final: 0.7689 (m-80)
REVERT: D   85 LYS cc_start: 0.8975 (mttt) cc_final: 0.8614 (mmtt)
REVERT: D  121 TYR cc_start: 0.9168 (t80) cc_final: 0.8792 (t80)
REVERT: E   97 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8648 (mm-30)
REVERT: E  111 TYR cc_start: 0.9525 (t80) cc_final: 0.9303 (t80)
REVERT: F   88 TYR cc_start: 0.7417 (m-10) cc_final: 0.6449 (m-10)
REVERT: G   57 TYR cc_start: 0.8692 (t80) cc_final: 0.8394 (t80)
REVERT: H   71 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: H   83 TYR cc_start: 0.8747 (m-10) cc_final: 0.8503 (m-80)
REVERT: H  120 LYS cc_start: 0.9042 (ptmm) cc_final: 0.8716 (ptmm)
REVERT: K  667 TYR cc_start: 0.8687 (p90) cc_final: 0.8223 (p90)
REVERT: M   22 MET cc_start: 0.8622 (pmm) cc_final: 0.8319 (pmm)
REVERT: M   57 GLU cc_start: 0.8139 (pt0) cc_final: 0.7884 (pp20)
REVERT: M   58 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6974 (mm-30)
REVERT: N   22 MET cc_start: 0.8021 (mpp) cc_final: 0.7819 (mpp)
REVERT: N  119 THR cc_start: 0.9475 (m) cc_final: 0.9017 (p)
REVERT: N  122 PHE cc_start: 0.7378 (m-80) cc_final: 0.6895 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 275
  average time/residue: 0.1333
  time to fit residues: 52.9476
Evaluate side-chains
  210 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 80 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 117 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 87 optimal weight:    6.9990
   chunk 82 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
M  50 HIS
M 128 ASN
M 188 HIS
N  35 GLN
N  50 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.073069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.054441 restraints weight = 53379.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.055103 restraints weight = 40075.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.055235 restraints weight = 33623.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.055449 restraints weight = 28519.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.055497 restraints weight = 26023.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054  16588  Z= 0.310
  Angle     :  0.742  10.547  23646  Z= 0.413
  Chirality :  0.043   0.265   2659
  Planarity :  0.005   0.043   1979
  Dihedral  : 31.438 117.633   4522
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.22 %
    Favored  : 97.68 %
  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: -0.86 (0.24), residues: 1171
  helix:  0.11 (0.20), residues: 670
  sheet: -0.37 (0.52), residues: 86
  loop : -1.64 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  11 
 TYR   0.039   0.002   TYR B  51 
 PHE   0.021   0.002   PHE E  79 
 TRP   0.044   0.003   TRP M 131 
 HIS   0.008   0.002   HIS N  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 (16588)
  covalent geometry    : angle       0.74215 (23646)
  hydrogen bonds       : bond        0.05446 (  837)
  hydrogen bonds       : angle       3.79545 ( 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
  246 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.7842 (pp20) cc_final: 0.7613 (pp20)
REVERT: A   74 GLU cc_start: 0.8511 (tt0) cc_final: 0.8148 (tt0)
REVERT: B   25 ASN cc_start: 0.8081 (t0) cc_final: 0.7679 (t0)
REVERT: B   31 LYS cc_start: 0.8639 (tppp) cc_final: 0.8100 (tppp)
REVERT: B   85 ASP cc_start: 0.8608 (m-30) cc_final: 0.8326 (m-30)
REVERT: B   88 TYR cc_start: 0.6886 (m-80) cc_final: 0.6302 (m-80)
REVERT: C   24 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7771 (tp-100)
REVERT: C   41 GLU cc_start: 0.8628 (pm20) cc_final: 0.8262 (mp0)
REVERT: C   56 GLU cc_start: 0.7947 (tt0) cc_final: 0.7640 (tt0)
REVERT: C   57 TYR cc_start: 0.8774 (t80) cc_final: 0.8466 (t80)
REVERT: C   61 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8166 (tp30)
REVERT: D   62 MET cc_start: 0.9337 (mmm) cc_final: 0.9026 (tpp)
REVERT: D   67 ASN cc_start: 0.9162 (m-40) cc_final: 0.8702 (t0)
REVERT: D   85 LYS cc_start: 0.9083 (mttt) cc_final: 0.8708 (mmtt)
REVERT: D  121 TYR cc_start: 0.9173 (t80) cc_final: 0.8821 (t80)
REVERT: E   97 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8629 (mm-30)
REVERT: F   63 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: G   56 GLU cc_start: 0.7886 (pt0) cc_final: 0.7645 (tt0)
REVERT: H   51 ASP cc_start: 0.8294 (t0) cc_final: 0.8019 (t0)
REVERT: H   71 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: H   83 TYR cc_start: 0.8894 (m-10) cc_final: 0.8626 (m-10)
REVERT: H   86 ARG cc_start: 0.8646 (mpt90) cc_final: 0.8356 (mtt-85)
REVERT: H  120 LYS cc_start: 0.9212 (ptmm) cc_final: 0.8856 (ptmm)
REVERT: M   22 MET cc_start: 0.8587 (pmm) cc_final: 0.8345 (pmm)
REVERT: M   56 CYS cc_start: 0.8000 (m) cc_final: 0.7733 (m)
REVERT: N  119 THR cc_start: 0.9472 (m) cc_final: 0.8993 (p)
REVERT: N  122 PHE cc_start: 0.7518 (m-80) cc_final: 0.7081 (m-80)
REVERT: N  195 HIS cc_start: 0.8002 (p-80) cc_final: 0.7548 (p-80)
  outliers start: 1
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1354
  time to fit residues: 47.7218
Evaluate side-chains
  195 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 30 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 137 optimal weight:   10.0000
   chunk 134 optimal weight:    0.0050
   chunk 95 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
A 137 GLN
B  75 HIS
C  73 ASN
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
H  82 HIS
M  50 HIS
M 128 ASN
N  35 GLN
N  50 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.076776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.058461 restraints weight = 53042.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.058711 restraints weight = 37648.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.059176 restraints weight = 30441.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.059407 restraints weight = 27244.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.059475 restraints weight = 25145.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.4982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  16588  Z= 0.147
  Angle     :  0.634   9.263  23646  Z= 0.359
  Chirality :  0.038   0.224   2659
  Planarity :  0.004   0.037   1979
  Dihedral  : 31.058 126.547   4522
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  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: -0.41 (0.24), residues: 1171
  helix:  0.50 (0.21), residues: 655
  sheet: -0.09 (0.56), residues: 74
  loop : -1.42 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.015   0.001   TYR D  40 
 PHE   0.015   0.001   PHE A  79 
 TRP   0.032   0.002   TRP M 131 
 HIS   0.010   0.001   HIS N  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (16588)
  covalent geometry    : angle       0.63430 (23646)
  hydrogen bonds       : bond        0.04248 (  837)
  hydrogen bonds       : angle       3.33013 ( 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
  271 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 269
  time to evaluate  : 0.459 
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: A   60 GLU cc_start: 0.7800 (pp20) cc_final: 0.7511 (pp20)
REVERT: A   74 GLU cc_start: 0.8596 (tt0) cc_final: 0.8179 (tt0)
REVERT: B   63 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8125 (mt-10)
REVERT: C   34 LEU cc_start: 0.9512 (tp) cc_final: 0.9259 (tp)
REVERT: C   41 GLU cc_start: 0.8493 (pm20) cc_final: 0.8126 (mp0)
REVERT: C   56 GLU cc_start: 0.7791 (tt0) cc_final: 0.7402 (tt0)
REVERT: D   62 MET cc_start: 0.9108 (mmm) cc_final: 0.8850 (tpp)
REVERT: D   67 ASN cc_start: 0.9002 (m-40) cc_final: 0.8655 (t0)
REVERT: D   85 LYS cc_start: 0.9080 (mttt) cc_final: 0.8766 (mmtt)
REVERT: D   93 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8657 (mm-30)
REVERT: D  121 TYR cc_start: 0.9161 (t80) cc_final: 0.8605 (t80)
REVERT: E   97 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8741 (mm-30)
REVERT: E  111 TYR cc_start: 0.9497 (t80) cc_final: 0.9112 (t80)
REVERT: F   72 TYR cc_start: 0.9333 (m-80) cc_final: 0.9030 (m-80)
REVERT: F   88 TYR cc_start: 0.7274 (m-10) cc_final: 0.6506 (m-10)
REVERT: F   98 TYR cc_start: 0.9044 (m-80) cc_final: 0.8801 (m-10)
REVERT: H   71 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7413 (tm-30)
REVERT: H   83 TYR cc_start: 0.8714 (m-10) cc_final: 0.8468 (m-80)
REVERT: H  120 LYS cc_start: 0.9023 (ptmm) cc_final: 0.8651 (ptmm)
REVERT: K  667 TYR cc_start: 0.8589 (p90) cc_final: 0.8131 (p90)
REVERT: M   22 MET cc_start: 0.8644 (pmm) cc_final: 0.8281 (pmm)
REVERT: M   56 CYS cc_start: 0.7835 (m) cc_final: 0.7504 (m)
REVERT: M   57 GLU cc_start: 0.8205 (pt0) cc_final: 0.7937 (pp20)
REVERT: M   58 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6087 (mm-30)
REVERT: M  191 GLU cc_start: 0.8061 (pm20) cc_final: 0.7660 (pm20)
REVERT: N   22 MET cc_start: 0.8180 (mpp) cc_final: 0.7974 (mpp)
REVERT: N  119 THR cc_start: 0.9426 (m) cc_final: 0.8932 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 270
  average time/residue: 0.1338
  time to fit residues: 52.1699
Evaluate side-chains
  203 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  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 79 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
B  75 HIS
C  73 ASN
D 109 HIS
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 128 ASN
N  35 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.077401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.058994 restraints weight = 52810.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.059079 restraints weight = 36996.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.059472 restraints weight = 31080.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.059732 restraints weight = 28184.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.059797 restraints weight = 25700.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.5181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  16588  Z= 0.150
  Angle     :  0.630   9.324  23646  Z= 0.355
  Chirality :  0.038   0.202   2659
  Planarity :  0.004   0.043   1979
  Dihedral  : 30.966 131.376   4522
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.77 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.24), residues: 1171
  helix:  0.61 (0.21), residues: 653
  sheet: -0.15 (0.57), residues: 74
  loop : -1.32 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  86 
 TYR   0.037   0.001   TYR B  51 
 PHE   0.013   0.001   PHE N 205 
 TRP   0.026   0.002   TRP M 131 
 HIS   0.013   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (16588)
  covalent geometry    : angle       0.62973 (23646)
  hydrogen bonds       : bond        0.04331 (  837)
  hydrogen bonds       : angle       3.31395 ( 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
  253 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.449 
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: A   60 GLU cc_start: 0.7863 (pp20) cc_final: 0.7602 (pp20)
REVERT: A   74 GLU cc_start: 0.8525 (tt0) cc_final: 0.8158 (tt0)
REVERT: B   63 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8134 (mt-10)
REVERT: C   34 LEU cc_start: 0.9536 (tp) cc_final: 0.9300 (tp)
REVERT: C   41 GLU cc_start: 0.8474 (pm20) cc_final: 0.8080 (mp0)
REVERT: C   92 GLU cc_start: 0.7449 (tt0) cc_final: 0.7001 (tm-30)
REVERT: D   67 ASN cc_start: 0.8912 (m-40) cc_final: 0.8703 (t0)
REVERT: D   85 LYS cc_start: 0.9043 (mttt) cc_final: 0.8632 (mmtt)
REVERT: D   86 ARG cc_start: 0.8863 (mpt-90) cc_final: 0.8526 (mtt-85)
REVERT: D  121 TYR cc_start: 0.9222 (t80) cc_final: 0.8725 (t80)
REVERT: E   97 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8495 (mm-30)
REVERT: E  111 TYR cc_start: 0.9486 (t80) cc_final: 0.8977 (t80)
REVERT: F   72 TYR cc_start: 0.9258 (m-80) cc_final: 0.8956 (m-80)
REVERT: F   98 TYR cc_start: 0.8998 (m-80) cc_final: 0.8718 (m-10)
REVERT: G   23 LEU cc_start: 0.8791 (mm) cc_final: 0.8159 (mm)
REVERT: G   56 GLU cc_start: 0.7297 (pt0) cc_final: 0.6754 (pt0)
REVERT: H   71 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7426 (tm-30)
REVERT: H  120 LYS cc_start: 0.9026 (ptmm) cc_final: 0.8630 (ptmm)
REVERT: K  667 TYR cc_start: 0.8737 (p90) cc_final: 0.8246 (p90)
REVERT: M   22 MET cc_start: 0.8617 (pmm) cc_final: 0.8275 (pmm)
REVERT: M   56 CYS cc_start: 0.7797 (m) cc_final: 0.7467 (m)
REVERT: M   57 GLU cc_start: 0.8204 (pt0) cc_final: 0.7915 (pp20)
REVERT: M   58 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6041 (mm-30)
REVERT: N   22 MET cc_start: 0.8182 (mpp) cc_final: 0.7967 (mpp)
REVERT: N  119 THR cc_start: 0.9418 (m) cc_final: 0.8906 (p)
REVERT: N  178 MET cc_start: 0.7353 (ttt) cc_final: 0.7040 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1281
  time to fit residues: 46.9838
Evaluate side-chains
  209 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 56 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
D 109 HIS
G  73 ASN
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
M 121 ASN
M 128 ASN
M 188 HIS
N  50 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.079049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.060671 restraints weight = 52914.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.060994 restraints weight = 36745.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.061369 restraints weight = 30438.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.061660 restraints weight = 27652.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.061781 restraints weight = 25252.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16588  Z= 0.141
  Angle     :  0.616   9.298  23646  Z= 0.347
  Chirality :  0.037   0.169   2659
  Planarity :  0.004   0.050   1979
  Dihedral  : 30.778 133.556   4522
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.58 %
    Favored  : 99.13 %
  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: -0.04 (0.25), residues: 1171
  helix:  0.80 (0.21), residues: 652
  sheet:  0.05 (0.57), residues: 74
  loop : -1.24 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L 669 
 TYR   0.040   0.002   TYR H  83 
 PHE   0.016   0.001   PHE A  79 
 TRP   0.017   0.002   TRP M 131 
 HIS   0.010   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (16588)
  covalent geometry    : angle       0.61610 (23646)
  hydrogen bonds       : bond        0.04134 (  837)
  hydrogen bonds       : angle       3.20555 ( 2112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2058.90 seconds
wall clock time: 36 minutes 26.07 seconds (2186.07 seconds total)