Starting phenix.real_space_refine
on Fri Feb 14 19:11:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j62_35999/02_2025/8j62_35999.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j62_35999/02_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_35999/02_2025/8j62_35999.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j62_35999/02_2025/8j62_35999.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j62_35999/02_2025/8j62_35999.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j62_35999/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.01, per 1000 atoms: 0.67
  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: 2.45
  Conformation dependent library (CDL) restraints added in 1.2 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: 3.88
  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: 3.81

  Time building geometry restraints manager: 2.82 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: 0.05
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:             4.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     33.440
  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:             0.000
  Load rotamer database and sin/cos tables:15.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.630
-------------------------------------------------------------------------------
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  10822  Z= 0.118
  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 

*********************** 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  : 1.227 
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: 1.4250
  time to fit residues: 516.2561
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  : 1.222 
-------------------------------------------------------------------------------
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 = 0.120892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.093539 restraints weight = 17977.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.51
r_work: 0.3387 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
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  10822  Z= 0.263
  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 

*********************** 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  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7858 (ttm110)
REVERT: A  136 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7803 (m110)
REVERT: C  167 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8167 (ttm-80)
REVERT: D   28 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8193 (ptmm)
REVERT: D  122 MET cc_start: 0.8834 (mmp) cc_final: 0.8576 (mmp)
REVERT: E   17 ARG cc_start: 0.8742 (mtt-85) cc_final: 0.8391 (ttp-170)
REVERT: E   88 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6683 (tm-30)
REVERT: G   99 ASP cc_start: 0.8074 (p0) cc_final: 0.7834 (p0)
REVERT: G  101 ASP cc_start: 0.8609 (m-30) cc_final: 0.8221 (p0)
REVERT: G  108 HIS cc_start: 0.8457 (m-70) cc_final: 0.8189 (t-90)
REVERT: H  122 MET cc_start: 0.8801 (mmp) cc_final: 0.8530 (mmp)
REVERT: I   17 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8483 (mtt-85)
REVERT: I   88 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6609 (tm-30)
  outliers start: 53
  outliers final: 28
  residues processed: 289
  average time/residue: 1.4119
  time to fit residues: 434.6405
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  : 1.237 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.118061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.090176 restraints weight = 18219.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.61
r_work: 0.3326 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10822  Z= 0.346
  Angle     :  0.602   6.642  14854  Z= 0.318
  Chirality :  0.046   0.167   1594
  Planarity :  0.004   0.027   1728
  Dihedral  : 15.140 167.464   1854
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 25.95 %
    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:  1.61 (0.25), residues: 1130
  helix:  1.73 (0.26), residues: 376
  sheet:  0.61 (0.27), residues: 324
  loop :  1.06 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP J 113 
 HIS   0.004   0.001   HIS G  56 
 PHE   0.009   0.001   PHE A 140 
 TYR   0.011   0.001   TYR G 111 
 ARG   0.007   0.001   ARG D  49 

*********************** 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
  307 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 242
  time to evaluate  : 1.177 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8193 (mt-10)
REVERT: A  166 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8288 (mp10)
REVERT: C  167 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8176 (ttm-80)
REVERT: D   30 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8032 (m)
REVERT: E   12 GLN cc_start: 0.8370 (mp10) cc_final: 0.8128 (mp10)
REVERT: E   88 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6874 (tm-30)
REVERT: E   97 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7235 (mp10)
REVERT: B  166 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8263 (mp10)
REVERT: G  108 HIS cc_start: 0.8516 (m-70) cc_final: 0.8262 (t-90)
REVERT: H   21 LEU cc_start: 0.8849 (mp) cc_final: 0.8576 (mp)
REVERT: H   30 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (m)
REVERT: I   12 GLN cc_start: 0.8340 (mp10) cc_final: 0.8070 (mp10)
  outliers start: 65
  outliers final: 36
  residues processed: 279
  average time/residue: 1.4503
  time to fit residues: 430.2584
Evaluate side-chains
  276 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 233
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
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  104 THR
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   85 VAL
Chi-restraints excluded: chain E residue   88 GLU
Chi-restraints excluded: chain E residue   97 GLN
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:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 71 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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**
J  41 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.121450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.094248 restraints weight = 18006.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.54
r_work: 0.3405 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10822  Z= 0.165
  Angle     :  0.564   9.356  14854  Z= 0.290
  Chirality :  0.042   0.155   1594
  Planarity :  0.004   0.029   1728
  Dihedral  : 15.030 165.844   1854
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 28.56 %
    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:  1.73 (0.25), residues: 1130
  helix:  1.89 (0.26), residues: 376
  sheet:  0.69 (0.27), residues: 328
  loop :  1.05 (0.33), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  89 
 HIS   0.004   0.001   HIS C 110 
 PHE   0.006   0.001   PHE B  58 
 TYR   0.020   0.001   TYR F  29 
 ARG   0.007   0.001   ARG H  90 

*********************** 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
  307 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 263
  time to evaluate  : 1.125 
Fit side-chains
REVERT: A   50 LEU cc_start: 0.9042 (mt) cc_final: 0.8797 (mm)
REVERT: A   57 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7835 (ttm110)
REVERT: A  136 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7948 (m110)
REVERT: A  166 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8167 (mp10)
REVERT: C   33 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7948 (mtp85)
REVERT: C  167 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8202 (ttm-80)
REVERT: D   35 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.8096 (mmm-85)
REVERT: E   12 GLN cc_start: 0.8313 (mp10) cc_final: 0.8075 (mp10)
REVERT: E   17 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8090 (mtm180)
REVERT: E   88 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6625 (tm-30)
REVERT: B   50 LEU cc_start: 0.9015 (mt) cc_final: 0.8764 (mm)
REVERT: B  166 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8115 (mp10)
REVERT: H   35 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8114 (mmm-85)
REVERT: I   12 GLN cc_start: 0.8325 (mp10) cc_final: 0.7961 (mp10)
REVERT: I   17 ARG cc_start: 0.8703 (mtt-85) cc_final: 0.8157 (ttp-170)
REVERT: J   69 PHE cc_start: 0.8470 (m-10) cc_final: 0.8167 (m-10)
  outliers start: 44
  outliers final: 24
  residues processed: 290
  average time/residue: 1.5094
  time to fit residues: 464.5726
Evaluate side-chains
  273 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 244
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
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  101 VAL
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain C residue   67 THR
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 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  166 GLN
Chi-restraints excluded: chain G residue   67 THR
Chi-restraints excluded: chain G residue   90 ARG
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  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:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.120572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.092984 restraints weight = 17828.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.55
r_work: 0.3374 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10822  Z= 0.216
  Angle     :  0.584   9.738  14854  Z= 0.299
  Chirality :  0.043   0.168   1594
  Planarity :  0.004   0.034   1728
  Dihedral  : 15.001 165.325   1854
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 28.16 %
    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:  1.78 (0.25), residues: 1130
  helix:  1.99 (0.26), residues: 376
  sheet:  0.74 (0.27), residues: 324
  loop :  1.00 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  89 
 HIS   0.006   0.001   HIS C 110 
 PHE   0.007   0.001   PHE A  58 
 TYR   0.010   0.001   TYR C  69 
 ARG   0.008   0.001   ARG D  49 

*********************** 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
  294 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 246
  time to evaluate  : 1.213 
Fit side-chains
REVERT: A   50 LEU cc_start: 0.9046 (mt) cc_final: 0.8823 (mm)
REVERT: A   57 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7857 (ttm110)
REVERT: A   89 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8214 (mtm110)
REVERT: A  136 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7980 (m110)
REVERT: A  166 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8134 (mp10)
REVERT: C   33 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7970 (mtp85)
REVERT: C  167 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8216 (ttm-80)
REVERT: E   12 GLN cc_start: 0.8278 (mp10) cc_final: 0.7947 (mp10)
REVERT: E   17 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8320 (ttp-170)
REVERT: B   50 LEU cc_start: 0.9041 (mt) cc_final: 0.8799 (mm)
REVERT: B   89 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8213 (mtm110)
REVERT: B  166 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8207 (mp10)
REVERT: G   88 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7457 (pt0)
REVERT: I   12 GLN cc_start: 0.8302 (mp10) cc_final: 0.7911 (mp10)
REVERT: I   17 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8293 (ttp-170)
  outliers start: 48
  outliers final: 32
  residues processed: 275
  average time/residue: 1.5561
  time to fit residues: 453.5974
Evaluate side-chains
  275 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 238
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
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  101 VAL
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 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   37 VAL
Chi-restraints excluded: chain B residue  101 VAL
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  107 ILE
Chi-restraints excluded: chain I residue  169 LEU
Chi-restraints excluded: chain J residue   97 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 30 optimal weight:    9.9990
   chunk 108 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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
** 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 = 0.3971 r_free = 0.3971 target = 0.118439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.090888 restraints weight = 18003.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.56
r_work: 0.3338 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  10822  Z= 0.291
  Angle     :  0.609   9.394  14854  Z= 0.314
  Chirality :  0.045   0.150   1594
  Planarity :  0.004   0.038   1728
  Dihedral  : 15.070 166.881   1854
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 27.35 %
    Favored  : 66.23 %
  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:  1.70 (0.25), residues: 1130
  helix:  1.92 (0.26), residues: 376
  sheet:  0.66 (0.28), residues: 326
  loop :  0.99 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  89 
 HIS   0.008   0.001   HIS G 110 
 PHE   0.008   0.001   PHE H  68 
 TYR   0.022   0.001   TYR J  29 
 ARG   0.009   0.001   ARG D  49 

*********************** 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
  309 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 245
  time to evaluate  : 1.166 
Fit side-chains
REVERT: A   50 LEU cc_start: 0.9080 (mt) cc_final: 0.8856 (mm)
REVERT: A   57 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7842 (ttm110)
REVERT: A   89 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8251 (mtm110)
REVERT: A   97 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8202 (mt-10)
REVERT: A  136 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7922 (m110)
REVERT: A  166 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8121 (mp10)
REVERT: C  167 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.8182 (ttm-80)
REVERT: D   20 LYS cc_start: 0.9358 (ttpp) cc_final: 0.9146 (tmmt)
REVERT: E   12 GLN cc_start: 0.8272 (mp10) cc_final: 0.7930 (mp10)
REVERT: E   17 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8277 (ttp-170)
REVERT: B   50 LEU cc_start: 0.9081 (mt) cc_final: 0.8845 (mm)
REVERT: B   89 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8247 (mtm110)
REVERT: B  166 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8173 (mp10)
REVERT: G   88 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7436 (pt0)
REVERT: H   20 LYS cc_start: 0.9406 (ttpp) cc_final: 0.9135 (tmmt)
REVERT: H   30 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7973 (m)
REVERT: I   12 GLN cc_start: 0.8231 (mp10) cc_final: 0.7792 (mp10)
REVERT: I   97 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7128 (mp10)
REVERT: I  171 GLU cc_start: 0.8378 (pp20) cc_final: 0.8151 (pm20)
  outliers start: 64
  outliers final: 37
  residues processed: 285
  average time/residue: 1.4505
  time to fit residues: 439.7641
Evaluate side-chains
  278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 233
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
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   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  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   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   58 VAL
Chi-restraints excluded: chain J residue   97 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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
G 110 HIS
** 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 = 0.3994 r_free = 0.3994 target = 0.120060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.092931 restraints weight = 18058.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.52
r_work: 0.3377 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10822  Z= 0.208
  Angle     :  0.589   9.484  14854  Z= 0.302
  Chirality :  0.043   0.145   1594
  Planarity :  0.004   0.044   1728
  Dihedral  : 15.022 165.961   1854
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 29.86 %
    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:  1.77 (0.25), residues: 1130
  helix:  2.01 (0.27), residues: 376
  sheet:  0.73 (0.28), residues: 324
  loop :  0.96 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  89 
 HIS   0.006   0.001   HIS G 110 
 PHE   0.007   0.001   PHE A  58 
 TYR   0.010   0.001   TYR C  69 
 ARG   0.009   0.001   ARG G  23 

*********************** 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
  293 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 244
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7835 (ttm110)
REVERT: A   86 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8332 (pttm)
REVERT: A   89 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8275 (mtm110)
REVERT: A  136 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7909 (m110)
REVERT: A  166 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8164 (mp10)
REVERT: C   33 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7914 (mtp85)
REVERT: C   88 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7432 (pt0)
REVERT: C  167 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8209 (ttm-80)
REVERT: D   20 LYS cc_start: 0.9347 (ttpp) cc_final: 0.9127 (tmmt)
REVERT: E   12 GLN cc_start: 0.8283 (mp10) cc_final: 0.7853 (mp10)
REVERT: E   17 ARG cc_start: 0.8633 (mtt180) cc_final: 0.8203 (ttp-170)
REVERT: B   86 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8347 (pttm)
REVERT: B   89 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8275 (mtm110)
REVERT: B  166 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8130 (mp10)
REVERT: G   88 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7413 (pt0)
REVERT: H   20 LYS cc_start: 0.9396 (ttpp) cc_final: 0.9102 (tmmt)
REVERT: I   12 GLN cc_start: 0.8256 (mp10) cc_final: 0.7826 (mp10)
  outliers start: 49
  outliers final: 34
  residues processed: 273
  average time/residue: 1.4147
  time to fit residues: 411.5052
Evaluate side-chains
  273 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 231
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
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   86 LYS
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   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   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   86 LYS
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   88 LEU
Chi-restraints excluded: chain H residue  106 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain J residue   97 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   chunk 51 optimal weight:   30.0000
   chunk 33 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.118643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.091115 restraints weight = 18100.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.57
r_work: 0.3344 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10822  Z= 0.274
  Angle     :  0.640   9.223  14854  Z= 0.323
  Chirality :  0.045   0.149   1594
  Planarity :  0.004   0.048   1728
  Dihedral  : 15.066 166.651   1854
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 29.56 %
    Favored  : 65.53 %
  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:  1.70 (0.25), residues: 1130
  helix:  1.93 (0.27), residues: 376
  sheet:  0.71 (0.28), residues: 320
  loop :  0.93 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  89 
 HIS   0.005   0.001   HIS G 110 
 PHE   0.007   0.001   PHE H  68 
 TYR   0.021   0.001   TYR J  29 
 ARG   0.011   0.001   ARG G  23 

*********************** 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
  290 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 241
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7904 (ttm110)
REVERT: A   89 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8318 (mtm110)
REVERT: A  136 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7929 (m110)
REVERT: A  166 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8164 (mp10)
REVERT: C   88 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7462 (pt0)
REVERT: C  167 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8209 (ttm-80)
REVERT: E   12 GLN cc_start: 0.8290 (mp10) cc_final: 0.7821 (mp10)
REVERT: E   97 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7247 (mp10)
REVERT: F   41 GLN cc_start: 0.8356 (mt0) cc_final: 0.8129 (mp10)
REVERT: B   89 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8317 (mtm110)
REVERT: B  166 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8153 (mp10)
REVERT: G   88 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7439 (pt0)
REVERT: I   12 GLN cc_start: 0.8243 (mp10) cc_final: 0.7790 (mp10)
REVERT: J   41 GLN cc_start: 0.8460 (mt0) cc_final: 0.8191 (mp10)
  outliers start: 49
  outliers final: 37
  residues processed: 271
  average time/residue: 1.4653
  time to fit residues: 421.8077
Evaluate side-chains
  277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 233
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
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  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   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   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  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:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.119994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.092652 restraints weight = 18042.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.58
r_work: 0.3371 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10822  Z= 0.211
  Angle     :  0.629  10.138  14854  Z= 0.317
  Chirality :  0.043   0.141   1594
  Planarity :  0.004   0.049   1728
  Dihedral  : 15.011 165.775   1854
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 30.26 %
    Favored  : 65.33 %
  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:  1.76 (0.26), residues: 1130
  helix:  2.11 (0.27), residues: 364
  sheet:  0.68 (0.28), residues: 324
  loop :  0.92 (0.32), residues: 442

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   0.010   0.001   TYR C  69 
 ARG   0.011   0.001   ARG D  90 

*********************** 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
  284 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 240
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7793 (ttm110)
REVERT: A   86 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8258 (pttm)
REVERT: A   89 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8263 (mtm110)
REVERT: A  136 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7803 (m110)
REVERT: A  166 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8102 (mp10)
REVERT: C   23 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7782 (mtt-85)
REVERT: C   33 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7978 (mtp85)
REVERT: C   88 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7400 (pt0)
REVERT: C  167 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.8174 (ttm-80)
REVERT: E   12 GLN cc_start: 0.8234 (mp10) cc_final: 0.7778 (mp10)
REVERT: F   41 GLN cc_start: 0.8359 (mt0) cc_final: 0.8150 (mp10)
REVERT: B   86 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8265 (pttm)
REVERT: B   89 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8259 (mtm110)
REVERT: B  166 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8104 (mp10)
REVERT: G   23 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7778 (mtt-85)
REVERT: G   88 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7402 (pt0)
REVERT: I   12 GLN cc_start: 0.8218 (mp10) cc_final: 0.7777 (mp10)
REVERT: J   41 GLN cc_start: 0.8445 (mt0) cc_final: 0.8150 (mp10)
  outliers start: 44
  outliers final: 33
  residues processed: 269
  average time/residue: 1.4788
  time to fit residues: 423.2530
Evaluate side-chains
  277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 238
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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  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   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   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  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   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   15 ARG
Chi-restraints excluded: chain I residue  107 ILE
Chi-restraints excluded: chain J residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 57 optimal weight:    8.9990
   chunk 110 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.118316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.090863 restraints weight = 18021.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.53
r_work: 0.3339 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10822  Z= 0.298
  Angle     :  0.674  10.201  14854  Z= 0.340
  Chirality :  0.045   0.147   1594
  Planarity :  0.004   0.047   1728
  Dihedral  : 15.079 167.614   1854
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 30.56 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.61 (0.25), residues: 1130
  helix:  1.88 (0.27), residues: 376
  sheet:  0.56 (0.28), residues: 322
  loop :  0.95 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  89 
 HIS   0.004   0.001   HIS G 110 
 PHE   0.008   0.001   PHE H  68 
 TYR   0.022   0.001   TYR F  29 
 ARG   0.010   0.001   ARG H  90 

********************** 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
  281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 238
  time to evaluate  : 1.190 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7892 (ttm110)
REVERT: A   86 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8260 (pttm)
REVERT: A   89 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8314 (mtm110)
REVERT: A  136 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7808 (m110)
REVERT: A  166 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8163 (mp10)
REVERT: C   23 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7816 (mtt-85)
REVERT: C   33 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7939 (mtp85)
REVERT: C   88 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7458 (pt0)
REVERT: C  167 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8189 (ttm-80)
REVERT: D   30 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8011 (m)
REVERT: D   52 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.8112 (mtp-110)
REVERT: E   12 GLN cc_start: 0.8259 (mp10) cc_final: 0.7765 (mp10)
REVERT: E   17 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8313 (mtp85)
REVERT: F   41 GLN cc_start: 0.8355 (mt0) cc_final: 0.8154 (mp10)
REVERT: B   86 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8270 (pttm)
REVERT: B   89 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8298 (mtm110)
REVERT: B  166 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8143 (mp10)
REVERT: G   23 ARG cc_start: 0.8234 (mtm110) cc_final: 0.7819 (mtt-85)
REVERT: G   88 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7457 (pt0)
REVERT: H   30 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8022 (m)
REVERT: H   52 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8078 (mtp-110)
REVERT: H   88 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8240 (mm)
REVERT: I   12 GLN cc_start: 0.8201 (mp10) cc_final: 0.7724 (mp10)
REVERT: J   41 GLN cc_start: 0.8354 (mt0) cc_final: 0.8086 (mp10)
  outliers start: 43
  outliers final: 33
  residues processed: 267
  average time/residue: 1.4351
  time to fit residues: 407.2546
Evaluate side-chains
  279 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 237
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
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  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   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  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   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  107 ILE
Chi-restraints excluded: chain J residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 90 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 87 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 54 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.119900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.092520 restraints weight = 17975.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.57
r_work: 0.3365 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10822  Z= 0.220
  Angle     :  0.638  10.093  14854  Z= 0.323
  Chirality :  0.043   0.140   1594
  Planarity :  0.004   0.036   1728
  Dihedral  : 15.013 166.568   1854
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 30.56 %
    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:  1.71 (0.26), residues: 1130
  helix:  2.10 (0.28), residues: 364
  sheet:  0.59 (0.28), residues: 324
  loop :  0.91 (0.32), residues: 442

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   0.008   0.001   PHE H  44 
 TYR   0.010   0.001   TYR G  69 
 ARG   0.010   0.001   ARG D  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9510.95 seconds
wall clock time: 168 minutes 58.24 seconds (10138.24 seconds total)