Starting phenix.real_space_refine
on Mon Jul 28 17:32:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j62_35999/07_2025/8j62_35999.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j62_35999/07_2025/8j62_35999.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2025/8j62_35999.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2025/8j62_35999.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2025/8j62_35999.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2025/8j62_35999.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      36      5.49       5
     S      48      5.16       5
     C    6578      2.51       5
     N    1826      2.21       5
     O    1958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10448
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1521
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 7, 'TRANS': 172}
    Chain: "C"
      Number of atoms: 1075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1075
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 120}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "D"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 844
          Classifications: {'peptide': 104}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 100}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "E"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 912
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 6, 'TRANS': 104}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "F"
      Number of atoms: 480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 480
          Classifications: {'peptide': 69}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 2, 'TRANS': 66}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 59
    Chain: "Y"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 391
          Classifications: {'RNA': 19}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 2, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 13, 'rna3p': 5}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'  U%rna3p_pyr:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    749  SG  CYS A  84      32.319  53.134  49.548  1.00 41.85           S
  ATOM    771  SG  CYS A  87      33.682  51.225  51.830  1.00 42.44           S

  Restraints were copied for chains:
    J, X, H, I, B, G
  Time building chain proxies: 7.17, per 1000 atoms: 0.69
  Number of scatterers: 10448
  At special positions: 0
  Unit cell: (86.0096, 109.933, 105.376, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      48     16.00
     P      36     15.00
     O    1958      8.00
     N    1826      7.00
     C    6578      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" ND1 HIS A  53 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  87 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  84 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B  87 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B  53 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B  84 "


  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2240

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 14 sheets defined
      35.9% alpha, 40.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 53 through 66
      removed outlier: 3.656A  pdb=" N   LYS A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 98
    Processing helix  chain 'A' and resid 115 through 128
    Processing helix  chain 'A' and resid 136 through 147
    Processing helix  chain 'A' and resid 160 through 177
    Processing helix  chain 'C' and resid 14 through 31
    Processing helix  chain 'C' and resid 42 through 46
      removed outlier: 3.566A  pdb=" N   SER C  46 " --> pdb=" O   HIS C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 111
    Processing helix  chain 'C' and resid 165 through 171
    Processing helix  chain 'D' and resid 18 through 24
      removed outlier: 3.898A  pdb=" N   GLU D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 50
    Processing helix  chain 'D' and resid 72 through 74
      No H-bonds generated for 'chain 'D' and resid 72 through 74'
    Processing helix  chain 'E' and resid 14 through 31
    Processing helix  chain 'E' and resid 42 through 46
      removed outlier: 3.516A  pdb=" N   GLU E  45 " --> pdb=" O   HIS E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 99 through 111
      removed outlier: 3.659A  pdb=" N   GLN E 105 " --> pdb=" O   ASP E 101 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   HIS E 110 " --> pdb=" O   LEU E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 165 through 171
      removed outlier: 3.556A  pdb=" N   LEU E 169 " --> pdb=" O   SER E 165 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 38 through 51
    Processing helix  chain 'F' and resid 70 through 74
    Processing helix  chain 'B' and resid 2 through 10
    Processing helix  chain 'B' and resid 53 through 66
      removed outlier: 3.656A  pdb=" N   LYS B  66 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 98
    Processing helix  chain 'B' and resid 115 through 128
    Processing helix  chain 'B' and resid 136 through 147
    Processing helix  chain 'B' and resid 160 through 177
    Processing helix  chain 'G' and resid 14 through 31
    Processing helix  chain 'G' and resid 42 through 46
      removed outlier: 3.566A  pdb=" N   SER G  46 " --> pdb=" O   HIS G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 99 through 111
    Processing helix  chain 'G' and resid 165 through 171
    Processing helix  chain 'H' and resid 18 through 24
      removed outlier: 3.898A  pdb=" N   GLU H  24 " --> pdb=" O   LYS H  20 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 36 through 50
    Processing helix  chain 'H' and resid 72 through 74
      No H-bonds generated for 'chain 'H' and resid 72 through 74'
    Processing helix  chain 'I' and resid 14 through 31
    Processing helix  chain 'I' and resid 42 through 46
      removed outlier: 3.516A  pdb=" N   GLU I  45 " --> pdb=" O   HIS I  42 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 99 through 111
      removed outlier: 3.659A  pdb=" N   GLN I 105 " --> pdb=" O   ASP I 101 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   HIS I 110 " --> pdb=" O   LEU I 106 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 165 through 171
      removed outlier: 3.558A  pdb=" N   LEU I 169 " --> pdb=" O   SER I 165 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 38 through 51
    Processing helix  chain 'J' and resid 70 through 74
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38
      removed outlier: 6.897A  pdb=" N   TRP A  81 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41
      removed outlier: 4.876A  pdb=" N   ILE C  87 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ILE C   9 " --> pdb=" O   ILE C  87 " (cutoff:3.500A)
      removed outlier: 11.423A  pdb=" N   TRP C  89 " --> pdb=" O   VAL C   7 " (cutoff:3.500A)
      removed outlier: 14.227A  pdb=" N   VAL C   7 " --> pdb=" O   TRP C  89 " (cutoff:3.500A)
      removed outlier: 18.909A  pdb=" N   LYS C  91 " --> pdb=" O   TRP C   5 " (cutoff:3.500A)
      removed outlier: 21.500A  pdb=" N   TRP C   5 " --> pdb=" O   LYS C  91 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   LEU D  64 " --> pdb=" O   ALA D  59 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE D  55 " --> pdb=" O   PHE D  68 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ASP D 120 " --> pdb=" O   ASP D 115 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41
      removed outlier: 11.324A  pdb=" N   SER C  95 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   ILE D 102 " --> pdb=" O   SER C  95 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 41
      removed outlier: 6.586A  pdb=" N   THR E  68 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLU E  54 " --> pdb=" O   ILE E  66 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE E  66 " --> pdb=" O   GLU E  54 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   HIS E  56 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU E  64 " --> pdb=" O   HIS E  56 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ALA E  62 " --> pdb=" O   PRO E  58 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   LEU E  64 " --> pdb=" O   ARG E  90 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ARG E  90 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   ILE E  66 " --> pdb=" O   GLU E  88 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLU E  88 " --> pdb=" O   ILE E  66 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   THR E  68 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   SER E  86 " --> pdb=" O   THR E  68 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   TRP E  70 " --> pdb=" O   GLY E  84 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   GLY E  84 " --> pdb=" O   TRP E  70 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 41
      removed outlier: 6.586A  pdb=" N   THR E  68 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLU E  54 " --> pdb=" O   ILE E  66 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE E  66 " --> pdb=" O   GLU E  54 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   HIS E  56 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU E  64 " --> pdb=" O   HIS E  56 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ALA E  62 " --> pdb=" O   PRO E  58 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   LEU E  64 " --> pdb=" O   ARG E  90 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ARG E  90 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   ILE E  66 " --> pdb=" O   GLU E  88 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLU E  88 " --> pdb=" O   ILE E  66 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   THR E  68 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   SER E  86 " --> pdb=" O   THR E  68 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   TRP E  70 " --> pdb=" O   GLY E  84 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   GLY E  84 " --> pdb=" O   TRP E  70 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLN E  83 " --> pdb=" O   VAL E  13 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   ILE E  87 " --> pdb=" O   ILE E   9 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ILE E   9 " --> pdb=" O   ILE E  87 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 96 through 103
    Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 38
    Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 38
      removed outlier: 6.898A  pdb=" N   TRP B  81 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41
      removed outlier: 4.877A  pdb=" N   ILE G  87 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ILE G   9 " --> pdb=" O   ILE G  87 " (cutoff:3.500A)
      removed outlier: 11.421A  pdb=" N   TRP G  89 " --> pdb=" O   VAL G   7 " (cutoff:3.500A)
      removed outlier: 14.228A  pdb=" N   VAL G   7 " --> pdb=" O   TRP G  89 " (cutoff:3.500A)
      removed outlier: 18.909A  pdb=" N   LYS G  91 " --> pdb=" O   TRP G   5 " (cutoff:3.500A)
      removed outlier: 21.500A  pdb=" N   TRP G   5 " --> pdb=" O   LYS G  91 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   LEU H  64 " --> pdb=" O   ALA H  59 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE H  55 " --> pdb=" O   PHE H  68 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ASP H 120 " --> pdb=" O   ASP H 115 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 39 through 41
      removed outlier: 11.323A  pdb=" N   SER G  95 " --> pdb=" O   PRO H 100 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   ILE H 102 " --> pdb=" O   SER G  95 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'I' and resid 39 through 41
      removed outlier: 6.585A  pdb=" N   THR I  68 " --> pdb=" O   SER I  52 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLU I  54 " --> pdb=" O   ILE I  66 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE I  66 " --> pdb=" O   GLU I  54 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   HIS I  56 " --> pdb=" O   LEU I  64 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LEU I  64 " --> pdb=" O   HIS I  56 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   ALA I  62 " --> pdb=" O   PRO I  58 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   LEU I  64 " --> pdb=" O   ARG I  90 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ARG I  90 " --> pdb=" O   LEU I  64 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   ILE I  66 " --> pdb=" O   GLU I  88 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLU I  88 " --> pdb=" O   ILE I  66 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   THR I  68 " --> pdb=" O   SER I  86 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   SER I  86 " --> pdb=" O   THR I  68 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   TRP I  70 " --> pdb=" O   GLY I  84 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   GLY I  84 " --> pdb=" O   TRP I  70 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'I' and resid 39 through 41
      removed outlier: 6.585A  pdb=" N   THR I  68 " --> pdb=" O   SER I  52 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLU I  54 " --> pdb=" O   ILE I  66 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE I  66 " --> pdb=" O   GLU I  54 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   HIS I  56 " --> pdb=" O   LEU I  64 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LEU I  64 " --> pdb=" O   HIS I  56 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   ALA I  62 " --> pdb=" O   PRO I  58 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   LEU I  64 " --> pdb=" O   ARG I  90 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ARG I  90 " --> pdb=" O   LEU I  64 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   ILE I  66 " --> pdb=" O   GLU I  88 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLU I  88 " --> pdb=" O   ILE I  66 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   THR I  68 " --> pdb=" O   SER I  86 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   SER I  86 " --> pdb=" O   THR I  68 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   TRP I  70 " --> pdb=" O   GLY I  84 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   GLY I  84 " --> pdb=" O   TRP I  70 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLN I  83 " --> pdb=" O   VAL I  13 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   ILE I  87 " --> pdb=" O   ILE I   9 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE I   9 " --> pdb=" O   ILE I  87 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'J' and resid 96 through 103

    582 hydrogen bonds defined for protein.
    1566 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.35

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3012
        1.34 -     1.45: 2237
        1.45 -     1.57: 5425
        1.57 -     1.69: 72
        1.69 -     1.81: 76
  Bond restraints: 10822
  Sorted by residual:
  bond pdb=" CA  TYR D  85 "
       pdb=" CB  TYR D  85 "
    ideal  model  delta    sigma   weight residual
    1.535  1.552 -0.017 2.09e-02 2.29e+03 6.29e-01
  bond pdb=" CA  TYR H  85 "
       pdb=" CB  TYR H  85 "
    ideal  model  delta    sigma   weight residual
    1.535  1.551 -0.016 2.09e-02 2.29e+03 5.61e-01
  bond pdb=" CA  GLY I  82 "
       pdb=" C   GLY I  82 "
    ideal  model  delta    sigma   weight residual
    1.522  1.515  0.007 1.06e-02 8.90e+03 4.67e-01
  bond pdb=" CA  GLY E  82 "
       pdb=" C   GLY E  82 "
    ideal  model  delta    sigma   weight residual
    1.522  1.515  0.007 1.06e-02 8.90e+03 4.47e-01
  bond pdb=" CB  GLU A 163 "
       pdb=" CG  GLU A 163 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 3.00e-02 1.11e+03 4.15e-01
  ... (remaining 10817 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 14447
        1.20 -     2.40: 304
        2.40 -     3.60: 93
        3.60 -     4.80: 8
        4.80 -     6.00: 2
  Bond angle restraints: 14854
  Sorted by residual:
  angle pdb=" C   VAL H  86 "
        pdb=" N   ASP H  87 "
        pdb=" CA  ASP H  87 "
      ideal   model   delta    sigma   weight residual
     121.75  118.21    3.54 1.73e+00 3.34e-01 4.19e+00
  angle pdb=" C3'   U Y  11 "
        pdb=" O3'   U Y  11 "
        pdb=" P     U Y  12 "
      ideal   model   delta    sigma   weight residual
     120.20  123.24   -3.04 1.50e+00 4.44e-01 4.11e+00
  angle pdb=" C   VAL D  86 "
        pdb=" N   ASP D  87 "
        pdb=" CA  ASP D  87 "
      ideal   model   delta    sigma   weight residual
     121.75  118.25    3.50 1.73e+00 3.34e-01 4.08e+00
  angle pdb=" C3'   U X  11 "
        pdb=" O3'   U X  11 "
        pdb=" P     U X  12 "
      ideal   model   delta    sigma   weight residual
     120.20  123.22   -3.02 1.50e+00 4.44e-01 4.06e+00
  angle pdb=" C   HIS I  28 "
        pdb=" N   MET I  29 "
        pdb=" CA  MET I  29 "
      ideal   model   delta    sigma   weight residual
     121.66  118.60    3.06 1.76e+00 3.23e-01 3.03e+00
  ... (remaining 14849 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.69: 5926
       32.69 -    65.37: 356
       65.37 -    98.06: 26
       98.06 -   130.74: 0
      130.74 -   163.43: 2
  Dihedral angle restraints: 6310
    sinusoidal: 2858
      harmonic: 3452
  Sorted by residual:
  dihedral pdb=" O4'   C Y   1 "
           pdb=" C1'   C Y   1 "
           pdb=" N1    C Y   1 "
           pdb=" C2    C Y   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   36.57  163.43     1      1.50e+01 4.44e-03 8.36e+01
  dihedral pdb=" O4'   C X   1 "
           pdb=" C1'   C X   1 "
           pdb=" N1    C X   1 "
           pdb=" C2    C X   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   36.64  163.36     1      1.50e+01 4.44e-03 8.35e+01
  dihedral pdb=" CB  GLU I  54 "
           pdb=" CG  GLU I  54 "
           pdb=" CD  GLU I  54 "
           pdb=" OE1 GLU I  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -90.15   90.15     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 6307 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 961
       0.027 -    0.053: 372
       0.053 -    0.080: 126
       0.080 -    0.106: 95
       0.106 -    0.133: 40
  Chirality restraints: 1594
  Sorted by residual:
  chirality pdb=" CA  ILE I  57 "
            pdb=" N   ILE I  57 "
            pdb=" C   ILE I  57 "
            pdb=" CB  ILE I  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE I  66 "
            pdb=" N   ILE I  66 "
            pdb=" C   ILE I  66 "
            pdb=" CB  ILE I  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  ILE E  57 "
            pdb=" N   ILE E  57 "
            pdb=" C   ILE E  57 "
            pdb=" CB  ILE E  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 1591 not shown)

  Planarity restraints: 1728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F 113 "   -0.011 2.00e-02 2.50e+03   1.21e-02 3.66e+00
        pdb=" CG  TRP F 113 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP F 113 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP F 113 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP F 113 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP F 113 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP F 113 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F 113 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F 113 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP F 113 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP J 113 "    0.011 2.00e-02 2.50e+03   1.18e-02 3.50e+00
        pdb=" CG  TRP J 113 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP J 113 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP J 113 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP J 113 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP J 113 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP J 113 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP J 113 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP J 113 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP J 113 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H  86 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.18e+00
        pdb=" C   VAL H  86 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   VAL H  86 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ASP H  87 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1725 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1205
        2.75 -     3.29: 9360
        3.29 -     3.83: 18363
        3.83 -     4.36: 22026
        4.36 -     4.90: 37780
  Nonbonded interactions: 88734
  Sorted by model distance:
  nonbonded pdb=" OG  SER H  53 "
            pdb=" O6    G Y  10 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER D  53 "
            pdb=" O6    G X  10 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OH  TYR A 112 "
            pdb=" OP1   U X   8 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR B 112 "
            pdb=" OP1   U Y   8 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" NH2 ARG G  23 "
            pdb=" OP2   C Y  17 "
     model   vdw
     2.239 3.120
  ... (remaining 88729 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'Y'
  selection = chain 'X'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     32.750
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
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      :  0.002   0.020  10828  Z= 0.092
  Angle     :  0.464   6.001  14854  Z= 0.252
  Chirality :  0.041   0.133   1594
  Planarity :  0.003   0.027   1728
  Dihedral  : 18.883 163.427   4070
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 24.35 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.25), residues: 1130
  helix:  1.85 (0.28), residues: 352
  sheet:  0.51 (0.27), residues: 326
  loop :  0.93 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP F 113 
 HIS   0.002   0.000   HIS H  37 
 PHE   0.007   0.001   PHE A  58 
 TYR   0.014   0.001   TYR D  85 
 ARG   0.006   0.000   ARG H 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13887 (  512)
  hydrogen bonds       : angle       6.21967 ( 1566)
  metal coordination   : bond        0.00103 (    6)
  covalent geometry    : bond        0.00184 (10822)
  covalent geometry    : angle       0.46417 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 323
  time to evaluate  : 1.153 
Fit side-chains
REVERT: C   99 ASP cc_start: 0.7721 (p0) cc_final: 0.7166 (p0)
REVERT: E   88 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: H   21 LEU cc_start: 0.8074 (mp) cc_final: 0.7857 (mp)
  outliers start: 29
  outliers final: 16
  residues processed: 341
  average time/residue: 1.4548
  time to fit residues: 528.2909
Evaluate side-chains
  277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 261
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain G residue   53 SER
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  114 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 87 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 90 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 67 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
C  43 HIS
D  45 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
G  43 HIS
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.120935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.093438 restraints weight = 17970.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.54
r_work: 0.3384 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10828  Z= 0.182
  Angle     :  0.568   5.777  14854  Z= 0.301
  Chirality :  0.044   0.152   1594
  Planarity :  0.004   0.028   1728
  Dihedral  : 15.130 163.411   1868
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 26.25 %
    Favored  : 68.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.25), residues: 1130
  helix:  1.74 (0.26), residues: 374
  sheet:  0.53 (0.26), residues: 330
  loop :  1.08 (0.33), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP J 113 
 HIS   0.004   0.001   HIS G  43 
 PHE   0.008   0.001   PHE B 140 
 TYR   0.017   0.001   TYR J  29 
 ARG   0.006   0.001   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03441 (  512)
  hydrogen bonds       : angle       5.08304 ( 1566)
  metal coordination   : bond        0.00381 (    6)
  covalent geometry    : bond        0.00411 (10822)
  covalent geometry    : angle       0.56754 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 260
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7826 (ttm110)
REVERT: A  136 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7765 (m110)
REVERT: C  167 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8152 (ttm-80)
REVERT: D   28 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8166 (ptmm)
REVERT: D  122 MET cc_start: 0.8800 (mmp) cc_final: 0.8543 (mmp)
REVERT: E   17 ARG cc_start: 0.8732 (mtt-85) cc_final: 0.8371 (ttp-170)
REVERT: E   88 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6615 (tm-30)
REVERT: G   99 ASP cc_start: 0.8040 (p0) cc_final: 0.7811 (p0)
REVERT: G  101 ASP cc_start: 0.8605 (m-30) cc_final: 0.8201 (p0)
REVERT: G  108 HIS cc_start: 0.8462 (m-70) cc_final: 0.8174 (t-90)
REVERT: H  122 MET cc_start: 0.8765 (mmp) cc_final: 0.8494 (mmp)
REVERT: I   17 ARG cc_start: 0.8723 (mtt-85) cc_final: 0.8467 (mtt-85)
REVERT: I   88 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6538 (tm-30)
  outliers start: 53
  outliers final: 28
  residues processed: 289
  average time/residue: 1.5611
  time to fit residues: 480.2025
Evaluate side-chains
  277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 244
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   41 ARG
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   88 GLU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  107 ILE
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   88 GLU
Chi-restraints excluded: chain I residue  169 LEU
Chi-restraints excluded: chain J residue   97 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
C 110 HIS
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.118384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.090509 restraints weight = 18215.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.61
r_work: 0.3332 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10828  Z= 0.225
  Angle     :  0.593   6.235  14854  Z= 0.313
  Chirality :  0.045   0.164   1594
  Planarity :  0.004   0.028   1728
  Dihedral  : 15.116 167.144   1854
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 26.25 %
    Favored  : 67.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.25), residues: 1130
  helix:  1.79 (0.26), residues: 374
  sheet:  0.64 (0.27), residues: 324
  loop :  1.05 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP J 113 
 HIS   0.004   0.001   HIS G  56 
 PHE   0.008   0.001   PHE B 140 
 TYR   0.011   0.001   TYR C  69 
 ARG   0.006   0.001   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  512)
  hydrogen bonds       : angle       5.08932 ( 1566)
  metal coordination   : bond        0.00472 (    6)
  covalent geometry    : bond        0.00510 (10822)
  covalent geometry    : angle       0.59295 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 242
  time to evaluate  : 1.752 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8189 (mt-10)
REVERT: A  166 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8285 (mp10)
REVERT: C  167 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8173 (ttm-80)
REVERT: D   30 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8032 (m)
REVERT: E   12 GLN cc_start: 0.8365 (mp10) cc_final: 0.8133 (mp10)
REVERT: E   88 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6865 (tm-30)
REVERT: B  166 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8261 (mp10)
REVERT: G  108 HIS cc_start: 0.8531 (m-70) cc_final: 0.8257 (t-90)
REVERT: H   21 LEU cc_start: 0.8833 (mp) cc_final: 0.8573 (mp)
REVERT: H   30 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8045 (m)
REVERT: I   12 GLN cc_start: 0.8338 (mp10) cc_final: 0.8073 (mp10)
  outliers start: 62
  outliers final: 35
  residues processed: 278
  average time/residue: 1.8051
  time to fit residues: 532.0942
Evaluate side-chains
  274 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 233
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   41 ARG
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue   88 GLU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   85 VAL
Chi-restraints excluded: chain I residue  169 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  108 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  41 GLN
B  96 GLN
** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  45 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.119249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.091548 restraints weight = 17868.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.55
r_work: 0.3352 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10828  Z= 0.182
  Angle     :  0.594   9.489  14854  Z= 0.306
  Chirality :  0.044   0.162   1594
  Planarity :  0.004   0.028   1728
  Dihedral  : 15.116 167.434   1854
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 26.65 %
    Favored  : 67.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.25), residues: 1130
  helix:  1.82 (0.26), residues: 376
  sheet:  0.55 (0.27), residues: 330
  loop :  1.05 (0.33), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  89 
 HIS   0.003   0.001   HIS C 110 
 PHE   0.007   0.001   PHE J  57 
 TYR   0.021   0.001   TYR F  29 
 ARG   0.008   0.001   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  512)
  hydrogen bonds       : angle       5.01061 ( 1566)
  metal coordination   : bond        0.00340 (    6)
  covalent geometry    : bond        0.00414 (10822)
  covalent geometry    : angle       0.59354 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 249
  time to evaluate  : 1.180 
Fit side-chains
REVERT: A   50 LEU cc_start: 0.9087 (mt) cc_final: 0.8837 (mm)
REVERT: A   57 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7897 (ttm110)
REVERT: A   97 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8173 (mt-10)
REVERT: A  136 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7973 (m110)
REVERT: A  166 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8184 (mp10)
REVERT: C   33 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7948 (mtp85)
REVERT: C  167 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8194 (ttm-80)
REVERT: D   20 LYS cc_start: 0.9354 (ttpp) cc_final: 0.9129 (tmmt)
REVERT: D   30 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8015 (m)
REVERT: E   12 GLN cc_start: 0.8302 (mp10) cc_final: 0.8051 (mp10)
REVERT: E   17 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8164 (mtm180)
REVERT: F   69 PHE cc_start: 0.8496 (m-10) cc_final: 0.8183 (m-10)
REVERT: B   50 LEU cc_start: 0.9077 (mt) cc_final: 0.8813 (mm)
REVERT: B  166 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8162 (mp10)
REVERT: G   88 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7524 (pt0)
REVERT: G  108 HIS cc_start: 0.8498 (m-70) cc_final: 0.8294 (t-90)
REVERT: H   20 LYS cc_start: 0.9386 (ttpp) cc_final: 0.9186 (tmmt)
REVERT: H   30 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.8018 (m)
REVERT: I   12 GLN cc_start: 0.8274 (mp10) cc_final: 0.7893 (mp10)
REVERT: I   17 ARG cc_start: 0.8717 (mtt-85) cc_final: 0.8119 (ttp-170)
REVERT: I   97 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7189 (mp10)
REVERT: J   69 PHE cc_start: 0.8511 (m-10) cc_final: 0.8207 (m-10)
  outliers start: 63
  outliers final: 32
  residues processed: 287
  average time/residue: 1.6347
  time to fit residues: 498.7974
Evaluate side-chains
  275 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 234
  time to evaluate  : 2.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   15 ARG
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   88 GLU
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   97 GLN
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain I residue  169 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  108 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 30 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  37 HIS
F  41 GLN
B  96 GLN
H  45 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.119286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.091694 restraints weight = 17812.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.53
r_work: 0.3353 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10828  Z= 0.175
  Angle     :  0.598   9.841  14854  Z= 0.307
  Chirality :  0.044   0.161   1594
  Planarity :  0.004   0.036   1728
  Dihedral  : 15.102 167.190   1854
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 26.35 %
    Favored  : 67.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.25), residues: 1130
  helix:  1.95 (0.27), residues: 364
  sheet:  0.58 (0.27), residues: 328
  loop :  0.93 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  89 
 HIS   0.007   0.001   HIS C 110 
 PHE   0.007   0.001   PHE H  57 
 TYR   0.010   0.001   TYR G  69 
 ARG   0.008   0.001   ARG G  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03220 (  512)
  hydrogen bonds       : angle       4.98625 ( 1566)
  metal coordination   : bond        0.00322 (    6)
  covalent geometry    : bond        0.00400 (10822)
  covalent geometry    : angle       0.59765 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 243
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.9072 (mt) cc_final: 0.8835 (mm)
REVERT: A   57 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7869 (ttm110)
REVERT: A   97 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8187 (mt-10)
REVERT: A  136 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7961 (m110)
REVERT: A  166 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8203 (mp10)
REVERT: C  167 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8211 (ttm-80)
REVERT: D   30 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.8029 (m)
REVERT: D   35 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.8046 (mmm-85)
REVERT: E   12 GLN cc_start: 0.8271 (mp10) cc_final: 0.7939 (mp10)
REVERT: E   17 ARG cc_start: 0.8680 (mtt180) cc_final: 0.8392 (ttp-170)
REVERT: E   97 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7250 (mp10)
REVERT: B   50 LEU cc_start: 0.9062 (mt) cc_final: 0.8815 (mm)
REVERT: B   89 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8240 (mtm110)
REVERT: B  166 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8189 (mp10)
REVERT: G   88 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7475 (pt0)
REVERT: H   20 LYS cc_start: 0.9373 (ttpp) cc_final: 0.9140 (tmmt)
REVERT: H   30 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8029 (m)
REVERT: I   12 GLN cc_start: 0.8283 (mp10) cc_final: 0.7795 (mp10)
REVERT: I   97 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7191 (mp10)
  outliers start: 64
  outliers final: 37
  residues processed: 280
  average time/residue: 2.3408
  time to fit residues: 701.5630
Evaluate side-chains
  281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 234
  time to evaluate  : 2.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   15 ARG
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   88 GLU
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   15 ARG
Chi-restraints excluded: chain I residue   97 GLN
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain I residue  169 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  108 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 108 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 55 optimal weight:    0.4980
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.119200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.091456 restraints weight = 17952.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.55
r_work: 0.3347 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10828  Z= 0.176
  Angle     :  0.592   8.126  14854  Z= 0.305
  Chirality :  0.044   0.145   1594
  Planarity :  0.004   0.040   1728
  Dihedral  : 15.097 167.143   1854
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 26.95 %
    Favored  : 66.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.25), residues: 1130
  helix:  1.97 (0.27), residues: 364
  sheet:  0.66 (0.28), residues: 324
  loop :  0.88 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  89 
 HIS   0.007   0.001   HIS G 110 
 PHE   0.007   0.001   PHE H  68 
 TYR   0.022   0.001   TYR J  29 
 ARG   0.009   0.001   ARG G  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03133 (  512)
  hydrogen bonds       : angle       4.92131 ( 1566)
  metal coordination   : bond        0.00328 (    6)
  covalent geometry    : bond        0.00402 (10822)
  covalent geometry    : angle       0.59212 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 237
  time to evaluate  : 1.190 
Fit side-chains
REVERT: A   50 LEU cc_start: 0.9056 (mt) cc_final: 0.8836 (mm)
REVERT: A   57 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7891 (ttm110)
REVERT: A   89 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8228 (mtm110)
REVERT: A   97 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8199 (mt-10)
REVERT: A  136 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7987 (m110)
REVERT: A  166 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8124 (mp10)
REVERT: C   88 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7458 (pt0)
REVERT: C  167 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8207 (ttm-80)
REVERT: D   30 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8017 (m)
REVERT: E   12 GLN cc_start: 0.8291 (mp10) cc_final: 0.7933 (mp10)
REVERT: E   97 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7214 (mp10)
REVERT: F   41 GLN cc_start: 0.8384 (mt0) cc_final: 0.8164 (mp10)
REVERT: B   50 LEU cc_start: 0.9074 (mt) cc_final: 0.8839 (mm)
REVERT: B   89 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8270 (mtm110)
REVERT: B  166 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8188 (mp10)
REVERT: G   88 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7429 (pt0)
REVERT: H   20 LYS cc_start: 0.9406 (ttpp) cc_final: 0.9122 (tmmt)
REVERT: H   30 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (m)
REVERT: H   88 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8202 (mm)
REVERT: I   12 GLN cc_start: 0.8278 (mp10) cc_final: 0.7775 (mp10)
REVERT: I   97 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7166 (mp10)
  outliers start: 64
  outliers final: 38
  residues processed: 281
  average time/residue: 1.4795
  time to fit residues: 442.1804
Evaluate side-chains
  281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 231
  time to evaluate  : 1.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  116 LEU
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   15 ARG
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   88 GLU
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   15 ARG
Chi-restraints excluded: chain I residue   97 GLN
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain I residue  169 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  108 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 97 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 72 optimal weight:    3.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
D  41 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
G 110 HIS
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.119182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.091506 restraints weight = 18037.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.55
r_work: 0.3349 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10828  Z= 0.173
  Angle     :  0.601   8.766  14854  Z= 0.308
  Chirality :  0.044   0.143   1594
  Planarity :  0.004   0.047   1728
  Dihedral  : 15.100 167.051   1854
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 28.56 %
    Favored  : 65.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.25), residues: 1130
  helix:  1.92 (0.27), residues: 376
  sheet:  0.66 (0.28), residues: 320
  loop :  0.93 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  89 
 HIS   0.007   0.001   HIS G 110 
 PHE   0.007   0.001   PHE H  57 
 TYR   0.010   0.001   TYR G  69 
 ARG   0.011   0.001   ARG G  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03109 (  512)
  hydrogen bonds       : angle       4.90108 ( 1566)
  metal coordination   : bond        0.00306 (    6)
  covalent geometry    : bond        0.00398 (10822)
  covalent geometry    : angle       0.60108 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 241
  time to evaluate  : 1.133 
Fit side-chains
REVERT: A   50 LEU cc_start: 0.9053 (mt) cc_final: 0.8853 (mm)
REVERT: A   57 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7883 (ttm110)
REVERT: A   89 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8258 (mtm110)
REVERT: A   97 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8190 (mt-10)
REVERT: A  136 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7950 (m110)
REVERT: A  166 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8157 (mp10)
REVERT: C   88 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7425 (pt0)
REVERT: C  167 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8211 (ttm-80)
REVERT: D   30 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.8034 (m)
REVERT: E   12 GLN cc_start: 0.8280 (mp10) cc_final: 0.7901 (mp10)
REVERT: E   97 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7200 (mp10)
REVERT: F   41 GLN cc_start: 0.8340 (mt0) cc_final: 0.8119 (mp10)
REVERT: B   50 LEU cc_start: 0.9067 (mt) cc_final: 0.8856 (mm)
REVERT: B   89 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8263 (mtm110)
REVERT: B  166 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8190 (mp10)
REVERT: G   88 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7434 (pt0)
REVERT: H   30 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8020 (m)
REVERT: I   12 GLN cc_start: 0.8279 (mp10) cc_final: 0.7772 (mp10)
REVERT: I   97 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7160 (mp10)
  outliers start: 57
  outliers final: 39
  residues processed: 280
  average time/residue: 1.4345
  time to fit residues: 426.8734
Evaluate side-chains
  280 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 230
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   15 ARG
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   88 GLU
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   15 ARG
Chi-restraints excluded: chain I residue   97 GLN
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  108 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    0.0060
   chunk 89 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.2004

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.119989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.092714 restraints weight = 18078.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.57
r_work: 0.3370 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10828  Z= 0.137
  Angle     :  0.598  10.297  14854  Z= 0.305
  Chirality :  0.043   0.140   1594
  Planarity :  0.004   0.050   1728
  Dihedral  : 15.042 166.405   1854
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 29.26 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.26), residues: 1130
  helix:  2.01 (0.27), residues: 376
  sheet:  0.65 (0.28), residues: 324
  loop :  0.96 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  89 
 HIS   0.005   0.001   HIS G 110 
 PHE   0.007   0.001   PHE A  58 
 TYR   0.020   0.001   TYR F  29 
 ARG   0.012   0.001   ARG G  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02912 (  512)
  hydrogen bonds       : angle       4.78454 ( 1566)
  metal coordination   : bond        0.00197 (    6)
  covalent geometry    : bond        0.00315 (10822)
  covalent geometry    : angle       0.59757 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 252
  time to evaluate  : 1.407 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7862 (ttm110)
REVERT: A   86 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8297 (pttm)
REVERT: A   89 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8274 (mtm110)
REVERT: A  136 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7927 (m110)
REVERT: A  166 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8139 (mp10)
REVERT: C   33 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7912 (mtp85)
REVERT: C   88 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7397 (pt0)
REVERT: C  167 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8216 (ttm-80)
REVERT: D   52 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7899 (mtp-110)
REVERT: E   12 GLN cc_start: 0.8279 (mp10) cc_final: 0.7832 (mp10)
REVERT: E   17 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7926 (ttp-170)
REVERT: F   41 GLN cc_start: 0.8340 (mt0) cc_final: 0.8129 (mp10)
REVERT: B   86 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8323 (pttm)
REVERT: B   89 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8291 (mtm110)
REVERT: B  166 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8131 (mp10)
REVERT: G   88 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7416 (pt0)
REVERT: I   12 GLN cc_start: 0.8317 (mp10) cc_final: 0.7833 (mp10)
REVERT: I   97 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7172 (mp10)
  outliers start: 53
  outliers final: 35
  residues processed: 290
  average time/residue: 1.3887
  time to fit residues: 428.7723
Evaluate side-chains
  278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 236
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  116 LEU
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   88 GLU
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   15 ARG
Chi-restraints excluded: chain I residue   97 GLN
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain J residue   97 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 109 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0270
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   overall best weight:    1.5442

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.119531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.092045 restraints weight = 18070.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.59
r_work: 0.3356 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10828  Z= 0.159
  Angle     :  0.637   9.627  14854  Z= 0.321
  Chirality :  0.044   0.186   1594
  Planarity :  0.004   0.055   1728
  Dihedral  : 15.034 166.210   1854
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 30.66 %
    Favored  : 64.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.25), residues: 1130
  helix:  1.99 (0.27), residues: 376
  sheet:  0.62 (0.28), residues: 324
  loop :  0.92 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  89 
 HIS   0.005   0.001   HIS G 110 
 PHE   0.008   0.001   PHE D  44 
 TYR   0.010   0.001   TYR G  69 
 ARG   0.012   0.001   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02984 (  512)
  hydrogen bonds       : angle       4.81801 ( 1566)
  metal coordination   : bond        0.00272 (    6)
  covalent geometry    : bond        0.00368 (10822)
  covalent geometry    : angle       0.63748 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 235
  time to evaluate  : 1.168 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7887 (ttm110)
REVERT: A   86 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8291 (pttm)
REVERT: A   89 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8269 (mtm110)
REVERT: A   97 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8209 (mt-10)
REVERT: A  136 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7894 (m110)
REVERT: A  166 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8176 (mp10)
REVERT: C   33 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7947 (mtp85)
REVERT: C   88 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7423 (pt0)
REVERT: C  167 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8209 (ttm-80)
REVERT: D   52 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.7912 (mtp-110)
REVERT: D   88 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8183 (mm)
REVERT: E   12 GLN cc_start: 0.8249 (mp10) cc_final: 0.7790 (mp10)
REVERT: E   17 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7942 (ttp-170)
REVERT: F   41 GLN cc_start: 0.8345 (mt0) cc_final: 0.8121 (mp10)
REVERT: B   86 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8316 (pttm)
REVERT: B   89 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8278 (mtm110)
REVERT: B  166 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8097 (mp10)
REVERT: G   88 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7433 (pt0)
REVERT: G   91 LYS cc_start: 0.8483 (tppp) cc_final: 0.8196 (tppt)
REVERT: H   52 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.7848 (mtp-110)
REVERT: I   12 GLN cc_start: 0.8299 (mp10) cc_final: 0.7801 (mp10)
REVERT: I   97 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7174 (mp10)
REVERT: J   41 GLN cc_start: 0.8908 (mt0) cc_final: 0.8684 (mp10)
  outliers start: 44
  outliers final: 34
  residues processed: 264
  average time/residue: 1.4041
  time to fit residues: 394.3306
Evaluate side-chains
  275 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 232
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   15 ARG
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   88 GLU
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   97 GLN
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  108 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 110 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 109 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
H  41 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.117065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.089465 restraints weight = 18048.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.57
r_work: 0.3311 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  10828  Z= 0.259
  Angle     :  0.700  10.349  14854  Z= 0.356
  Chirality :  0.047   0.183   1594
  Planarity :  0.004   0.055   1728
  Dihedral  : 15.191 169.056   1854
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 29.96 %
    Favored  : 65.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1130
  helix:  1.77 (0.26), residues: 378
  sheet:  0.44 (0.28), residues: 326
  loop :  0.97 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  79 
 HIS   0.004   0.001   HIS G 110 
 PHE   0.011   0.002   PHE B 140 
 TYR   0.025   0.002   TYR J  29 
 ARG   0.011   0.001   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03362 (  512)
  hydrogen bonds       : angle       4.99357 ( 1566)
  metal coordination   : bond        0.00530 (    6)
  covalent geometry    : bond        0.00593 (10822)
  covalent geometry    : angle       0.70009 (14854)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 238
  time to evaluate  : 1.137 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7985 (ttm110)
REVERT: A   89 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8256 (mtm110)
REVERT: A   97 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8204 (mt-10)
REVERT: A  136 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7829 (m110)
REVERT: A  166 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8211 (mp10)
REVERT: C   88 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7490 (pt0)
REVERT: C  167 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8161 (ttm-80)
REVERT: D   88 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8199 (mm)
REVERT: E   12 GLN cc_start: 0.8247 (mp10) cc_final: 0.7823 (mp10)
REVERT: E   17 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7827 (ttp-170)
REVERT: E  105 GLN cc_start: 0.8685 (mt0) cc_final: 0.8183 (mp10)
REVERT: F   41 GLN cc_start: 0.8314 (mt0) cc_final: 0.8070 (mp10)
REVERT: B   86 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8255 (pttm)
REVERT: B   89 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8261 (mtm110)
REVERT: B  166 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8138 (mp10)
REVERT: G   88 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7501 (pt0)
REVERT: H   30 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8046 (m)
REVERT: H   52 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.7947 (mtp-110)
REVERT: H   88 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8296 (mm)
REVERT: I   12 GLN cc_start: 0.8237 (mp10) cc_final: 0.7785 (mp10)
REVERT: I   97 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7067 (mp10)
REVERT: J   41 GLN cc_start: 0.8913 (mt0) cc_final: 0.8623 (mp10)
  outliers start: 48
  outliers final: 31
  residues processed: 272
  average time/residue: 1.4489
  time to fit residues: 418.6282
Evaluate side-chains
  279 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 236
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue   54 GLU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  118 ARG
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain E residue   15 ARG
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain G residue   47 THR
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   88 GLU
Chi-restraints excluded: chain G residue   90 ARG
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  166 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   54 GLU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue   15 ARG
Chi-restraints excluded: chain I residue   97 GLN
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  108 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0040
   chunk 57 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 ASN
B  96 GLN
** I  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.121207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.094054 restraints weight = 17982.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.60
r_work: 0.3389 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10828  Z= 0.121
  Angle     :  0.639  10.282  14854  Z= 0.321
  Chirality :  0.043   0.169   1594
  Planarity :  0.004   0.045   1728
  Dihedral  : 15.029 166.504   1854
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 31.56 %
    Favored  : 64.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1130
  helix:  1.95 (0.27), residues: 376
  sheet:  0.54 (0.28), residues: 324
  loop :  0.91 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  89 
 HIS   0.005   0.001   HIS G 110 
 PHE   0.008   0.001   PHE D  44 
 TYR   0.010   0.001   TYR G  69 
 ARG   0.010   0.001   ARG G  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02817 (  512)
  hydrogen bonds       : angle       4.77433 ( 1566)
  metal coordination   : bond        0.00101 (    6)
  covalent geometry    : bond        0.00278 (10822)
  covalent geometry    : angle       0.63885 (14854)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11098.09 seconds
wall clock time: 197 minutes 40.46 seconds (11860.46 seconds total)