Starting phenix.real_space_refine
on Thu Sep 18 13:58:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cz9_46064/09_2025/9cz9_46064.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cz9_46064/09_2025/9cz9_46064.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cz9_46064/09_2025/9cz9_46064.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cz9_46064/09_2025/9cz9_46064.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cz9_46064/09_2025/9cz9_46064.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cz9_46064/09_2025/9cz9_46064.cif"
  }
  resolution = 2.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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: 5
    Type Number    sf(0)   Gaussians
     Fe     24      7.16       5
     S      48      5.16       5
     C   10656      2.51       5
     N    2688      2.21       5
     O    3696      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17112
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 1379
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 170, 1374
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 8, 'TRANS': 161}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 170, 1374
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 8, 'TRANS': 161}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 1397
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' FE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 44
          Classifications: {'water': 44}
          Link IDs: {None: 43}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "C"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 46
          Classifications: {'water': 46}
          Link IDs: {None: 45}
    Chain: "D"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "E"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "F"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "G"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 46
          Classifications: {'water': 46}
          Link IDs: {None: 45}
    Chain: "H"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "I"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "J"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "K"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 45
          Classifications: {'water': 45}
          Link IDs: {None: 44}
    Chain: "L"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 44
          Classifications: {'water': 44}
          Link IDs: {None: 43}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L
  Time building chain proxies: 2.41, per 1000 atoms: 0.14
  Number of scatterers: 17112
  At special positions: 0
  Unit cell: (106.95, 112.47, 104.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe     24     26.01
     S      48     16.00
     O    3696      8.00
     N    2688      7.00
     C   10656      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 118 " - pdb=" SG BCYS A  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 118 " - pdb=" SG BCYS B  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 118 " - pdb=" SG BCYS C  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 118 " - pdb=" SG BCYS D  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E 118 " - pdb=" SG BCYS E  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS F 118 " - pdb=" SG BCYS F  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS G 118 " - pdb=" SG BCYS G  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H 118 " - pdb=" SG BCYS H  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS I 118 " - pdb=" SG BCYS I  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS J 118 " - pdb=" SG BCYS J  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS K 118 " - pdb=" SG BCYS K  94 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L 118 " - pdb=" SG BCYS L  94 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3888

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      75.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR A  38 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE A  52 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU A  54 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE A  55 " --> pdb=" O   ALA A  51 " (cutoff:3.500A)
      Proline residue:  A  72  - end of helix
    Processing helix  chain 'A' and resid 84 through 90
    Processing helix  chain 'A' and resid 104 through 128
    Processing helix  chain 'A' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU A 147 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 182
    Processing helix  chain 'B' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR B  38 " --> pdb=" O   TYR B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE B  52 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU B  54 " --> pdb=" O   GLU B  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE B  55 " --> pdb=" O   ALA B  51 " (cutoff:3.500A)
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 84 through 90
    Processing helix  chain 'B' and resid 104 through 128
    Processing helix  chain 'B' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU B 147 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 182
    Processing helix  chain 'C' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR C  38 " --> pdb=" O   TYR C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 77
      removed outlier: 3.941A  pdb=" N   ALA C  51 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE C  52 " --> pdb=" O   GLU C  48 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU C  54 " --> pdb=" O   GLU C  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
      Proline residue:  C  72  - end of helix
    Processing helix  chain 'C' and resid 84 through 90
    Processing helix  chain 'C' and resid 104 through 128
    Processing helix  chain 'C' and resid 134 through 161
      removed outlier: 3.666A  pdb=" N   GLU C 147 " --> pdb=" O   ALA C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 182
    Processing helix  chain 'D' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 77
      removed outlier: 3.941A  pdb=" N   ALA D  51 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE D  52 " --> pdb=" O   GLU D  48 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU D  54 " --> pdb=" O   GLU D  50 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   ILE D  55 " --> pdb=" O   ALA D  51 " (cutoff:3.500A)
      Proline residue:  D  72  - end of helix
    Processing helix  chain 'D' and resid 84 through 90
    Processing helix  chain 'D' and resid 104 through 128
    Processing helix  chain 'D' and resid 134 through 161
      removed outlier: 3.666A  pdb=" N   GLU D 147 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 182
    Processing helix  chain 'E' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR E  38 " --> pdb=" O   TYR E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA E  51 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE E  52 " --> pdb=" O   GLU E  48 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU E  54 " --> pdb=" O   GLU E  50 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   ILE E  55 " --> pdb=" O   ALA E  51 " (cutoff:3.500A)
      Proline residue:  E  72  - end of helix
    Processing helix  chain 'E' and resid 84 through 90
    Processing helix  chain 'E' and resid 104 through 128
    Processing helix  chain 'E' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU E 147 " --> pdb=" O   ALA E 143 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 182
    Processing helix  chain 'F' and resid 15 through 44
      removed outlier: 3.652A  pdb=" N   THR F  38 " --> pdb=" O   TYR F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA F  51 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE F  52 " --> pdb=" O   GLU F  48 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU F  54 " --> pdb=" O   GLU F  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE F  55 " --> pdb=" O   ALA F  51 " (cutoff:3.500A)
      Proline residue:  F  72  - end of helix
    Processing helix  chain 'F' and resid 84 through 90
    Processing helix  chain 'F' and resid 104 through 128
    Processing helix  chain 'F' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU F 147 " --> pdb=" O   ALA F 143 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 182
    Processing helix  chain 'G' and resid 15 through 44
      removed outlier: 3.652A  pdb=" N   THR G  38 " --> pdb=" O   TYR G  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA G  51 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE G  52 " --> pdb=" O   GLU G  48 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU G  54 " --> pdb=" O   GLU G  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE G  55 " --> pdb=" O   ALA G  51 " (cutoff:3.500A)
      Proline residue:  G  72  - end of helix
    Processing helix  chain 'G' and resid 84 through 90
    Processing helix  chain 'G' and resid 104 through 128
    Processing helix  chain 'G' and resid 134 through 161
      removed outlier: 3.666A  pdb=" N   GLU G 147 " --> pdb=" O   ALA G 143 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 178 through 182
    Processing helix  chain 'H' and resid 15 through 44
      removed outlier: 3.652A  pdb=" N   THR H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA H  51 " --> pdb=" O   LEU H  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE H  52 " --> pdb=" O   GLU H  48 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU H  54 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE H  55 " --> pdb=" O   ALA H  51 " (cutoff:3.500A)
      Proline residue:  H  72  - end of helix
    Processing helix  chain 'H' and resid 84 through 90
    Processing helix  chain 'H' and resid 104 through 128
    Processing helix  chain 'H' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU H 147 " --> pdb=" O   ALA H 143 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 178 through 182
    Processing helix  chain 'I' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR I  38 " --> pdb=" O   TYR I  34 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 45 through 77
      removed outlier: 3.941A  pdb=" N   ALA I  51 " --> pdb=" O   LEU I  47 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ILE I  52 " --> pdb=" O   GLU I  48 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU I  54 " --> pdb=" O   GLU I  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE I  55 " --> pdb=" O   ALA I  51 " (cutoff:3.500A)
      Proline residue:  I  72  - end of helix
    Processing helix  chain 'I' and resid 84 through 90
    Processing helix  chain 'I' and resid 104 through 128
    Processing helix  chain 'I' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU I 147 " --> pdb=" O   ALA I 143 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 178 through 182
    Processing helix  chain 'J' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR J  38 " --> pdb=" O   TYR J  34 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA J  51 " --> pdb=" O   LEU J  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE J  52 " --> pdb=" O   GLU J  48 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU J  54 " --> pdb=" O   GLU J  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE J  55 " --> pdb=" O   ALA J  51 " (cutoff:3.500A)
      Proline residue:  J  72  - end of helix
    Processing helix  chain 'J' and resid 84 through 90
    Processing helix  chain 'J' and resid 104 through 128
    Processing helix  chain 'J' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU J 147 " --> pdb=" O   ALA J 143 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 178 through 182
    Processing helix  chain 'K' and resid 15 through 44
      removed outlier: 3.652A  pdb=" N   THR K  38 " --> pdb=" O   TYR K  34 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA K  51 " --> pdb=" O   LEU K  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE K  52 " --> pdb=" O   GLU K  48 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU K  54 " --> pdb=" O   GLU K  50 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   ILE K  55 " --> pdb=" O   ALA K  51 " (cutoff:3.500A)
      Proline residue:  K  72  - end of helix
    Processing helix  chain 'K' and resid 84 through 90
    Processing helix  chain 'K' and resid 104 through 128
    Processing helix  chain 'K' and resid 134 through 161
      removed outlier: 3.667A  pdb=" N   GLU K 147 " --> pdb=" O   ALA K 143 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 178 through 182
    Processing helix  chain 'L' and resid 15 through 44
      removed outlier: 3.653A  pdb=" N   THR L  38 " --> pdb=" O   TYR L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 45 through 77
      removed outlier: 3.940A  pdb=" N   ALA L  51 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE L  52 " --> pdb=" O   GLU L  48 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU L  54 " --> pdb=" O   GLU L  50 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE L  55 " --> pdb=" O   ALA L  51 " (cutoff:3.500A)
      Proline residue:  L  72  - end of helix
    Processing helix  chain 'L' and resid 84 through 90
    Processing helix  chain 'L' and resid 104 through 128
    Processing helix  chain 'L' and resid 134 through 161
      removed outlier: 3.668A  pdb=" N   GLU L 147 " --> pdb=" O   ALA L 143 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 178 through 182

    1152 hydrogen bonds defined for protein.
    3372 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: 2.90

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 5495
        1.35 -     1.48: 4121
        1.48 -     1.61: 7280
        1.61 -     1.74: 0
        1.74 -     1.86: 60
  Bond restraints: 16956
  Sorted by residual:
  bond pdb=" CG  ARG G 169 "
       pdb=" CD  ARG G 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.056 3.00e-02 1.11e+03 3.45e+00
  bond pdb=" CG  ARG F 169 "
       pdb=" CD  ARG F 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.056 3.00e-02 1.11e+03 3.43e+00
  bond pdb=" CG  ARG H 169 "
       pdb=" CD  ARG H 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.41e+00
  bond pdb=" CG  ARG K 169 "
       pdb=" CD  ARG K 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.38e+00
  bond pdb=" CG  ARG A 169 "
       pdb=" CD  ARG A 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.37e+00
  ... (remaining 16951 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 21548
        1.68 -     3.36: 1252
        3.36 -     5.04: 132
        5.04 -     6.72: 36
        6.72 -     8.40: 48
  Bond angle restraints: 23016
  Sorted by residual:
  angle pdb=" C   GLY D 165 "
        pdb=" N   HIS D 166 "
        pdb=" CA  HIS D 166 "
      ideal   model   delta    sigma   weight residual
     122.92  115.90    7.02 1.76e+00 3.23e-01 1.59e+01
  angle pdb=" C   GLY L 165 "
        pdb=" N   HIS L 166 "
        pdb=" CA  HIS L 166 "
      ideal   model   delta    sigma   weight residual
     122.92  115.91    7.01 1.76e+00 3.23e-01 1.59e+01
  angle pdb=" C   GLY C 165 "
        pdb=" N   HIS C 166 "
        pdb=" CA  HIS C 166 "
      ideal   model   delta    sigma   weight residual
     122.92  115.92    7.00 1.76e+00 3.23e-01 1.58e+01
  angle pdb=" C   GLY H 165 "
        pdb=" N   HIS H 166 "
        pdb=" CA  HIS H 166 "
      ideal   model   delta    sigma   weight residual
     122.92  115.94    6.98 1.76e+00 3.23e-01 1.58e+01
  angle pdb=" C   GLY J 165 "
        pdb=" N   HIS J 166 "
        pdb=" CA  HIS J 166 "
      ideal   model   delta    sigma   weight residual
     122.92  115.94    6.98 1.76e+00 3.23e-01 1.57e+01
  ... (remaining 23011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 9371
       17.17 -    34.34: 769
       34.34 -    51.51: 84
       51.51 -    68.68: 36
       68.68 -    85.84: 36
  Dihedral angle restraints: 10296
    sinusoidal: 4212
      harmonic: 6084
  Sorted by residual:
  dihedral pdb=" CA  GLU H  80 "
           pdb=" C   GLU H  80 "
           pdb=" N   LEU H  81 "
           pdb=" CA  LEU H  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.85   16.15     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  GLU K  80 "
           pdb=" C   GLU K  80 "
           pdb=" N   LEU K  81 "
           pdb=" CA  LEU K  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.86   16.14     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  GLU J  80 "
           pdb=" C   GLU J  80 "
           pdb=" N   LEU J  81 "
           pdb=" CA  LEU J  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.88   16.12     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 10293 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1460
       0.037 -    0.074: 700
       0.074 -    0.111: 273
       0.111 -    0.148: 73
       0.148 -    0.185: 26
  Chirality restraints: 2532
  Sorted by residual:
  chirality pdb=" CG  LEU K  70 "
            pdb=" CB  LEU K  70 "
            pdb=" CD1 LEU K  70 "
            pdb=" CD2 LEU K  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.18 2.00e-01 2.50e+01 8.54e-01
  chirality pdb=" CG  LEU D  70 "
            pdb=" CB  LEU D  70 "
            pdb=" CD1 LEU D  70 "
            pdb=" CD2 LEU D  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.39e-01
  chirality pdb=" CG  LEU L  70 "
            pdb=" CB  LEU L  70 "
            pdb=" CD1 LEU L  70 "
            pdb=" CD2 LEU L  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.35e-01
  ... (remaining 2529 not shown)

  Planarity restraints: 2988
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H 166 "   -0.037 2.00e-02 2.50e+03   3.25e-02 1.58e+01
        pdb=" CG  HIS H 166 "    0.068 2.00e-02 2.50e+03
        pdb=" ND1 HIS H 166 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS H 166 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 HIS H 166 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE2 HIS H 166 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 166 "   -0.037 2.00e-02 2.50e+03   3.24e-02 1.58e+01
        pdb=" CG  HIS D 166 "    0.068 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 166 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 166 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 166 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 166 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G 166 "   -0.037 2.00e-02 2.50e+03   3.24e-02 1.58e+01
        pdb=" CG  HIS G 166 "    0.068 2.00e-02 2.50e+03
        pdb=" ND1 HIS G 166 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS G 166 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 HIS G 166 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE2 HIS G 166 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2985 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 395
        2.53 -     3.12: 13289
        3.12 -     3.71: 30574
        3.71 -     4.31: 44922
        4.31 -     4.90: 70080
  Nonbonded interactions: 159260
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L  30 "
            pdb="FE    FE L 201 "
     model   vdw
     1.937 2.260
  nonbonded pdb=" OE1 GLU C  30 "
            pdb="FE    FE C 201 "
     model   vdw
     1.937 2.260
  nonbonded pdb=" OE1 GLU K  30 "
            pdb="FE    FE K 201 "
     model   vdw
     1.937 2.260
  nonbonded pdb=" OE1 GLU I  30 "
            pdb="FE    FE I 201 "
     model   vdw
     1.937 2.260
  nonbonded pdb=" OE1 GLU G  30 "
            pdb="FE    FE G 201 "
     model   vdw
     1.938 2.260
  ... (remaining 159255 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             5.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     15.300
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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      :  0.006   0.056  16968  Z= 0.250
  Angle     :  0.948   8.398  23040  Z= 0.509
  Chirality :  0.052   0.185   2532
  Planarity :  0.009   0.050   2988
  Dihedral  : 13.778  85.844   6372
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.16), residues: 2040
  helix: -1.75 (0.11), residues: 1440
  sheet:  None (None), residues: 0
  loop : -0.13 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.033   0.004   ARG E  73 
 TYR   0.026   0.008   TYR I  98 
 PHE   0.032   0.009   PHE I 181 
 TRP   0.016   0.006   TRP I 154 
 HIS   0.026   0.007   HIS K 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 (16956)
  covalent geometry    : angle       0.94098 (23016)
  SS BOND              : bond        0.01989 (   12)
  SS BOND              : angle       3.73035 (   24)
  hydrogen bonds       : bond        0.18610 ( 1152)
  hydrogen bonds       : angle       8.27807 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6478 (tttt) cc_final: 0.5715 (ttpt)
REVERT: B  171 LYS cc_start: 0.6553 (tttt) cc_final: 0.5752 (ttpt)
REVERT: C  171 LYS cc_start: 0.6622 (tttt) cc_final: 0.5832 (ttpt)
REVERT: D  171 LYS cc_start: 0.6453 (tttt) cc_final: 0.5593 (ttpt)
REVERT: E  171 LYS cc_start: 0.6442 (tttt) cc_final: 0.5741 (ttpt)
REVERT: F  171 LYS cc_start: 0.6501 (tttt) cc_final: 0.5525 (tmtt)
REVERT: G  171 LYS cc_start: 0.6523 (tttt) cc_final: 0.5745 (ttpt)
REVERT: H  171 LYS cc_start: 0.6430 (tttt) cc_final: 0.5682 (ttpt)
REVERT: I  171 LYS cc_start: 0.6521 (tttt) cc_final: 0.5406 (pptt)
REVERT: J  171 LYS cc_start: 0.6496 (tttt) cc_final: 0.5477 (tmtt)
REVERT: K  171 LYS cc_start: 0.6429 (tttt) cc_final: 0.5693 (ttpt)
REVERT: L  171 LYS cc_start: 0.6529 (tttt) cc_final: 0.5719 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 300
  average time/residue: 0.8081
  time to fit residues: 264.2435
Evaluate side-chains
  244 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 194 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 200 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 107 ASN
** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 107 ASN
** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 107 ASN
** L 166 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 = 0.4168 r_free = 0.4168 target = 0.186673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.174365 restraints weight = 47487.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 1.32
r_work: 0.3881 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3758 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16968  Z= 0.166
  Angle     :  0.586   4.411  23040  Z= 0.329
  Chirality :  0.039   0.122   2532
  Planarity :  0.005   0.032   2988
  Dihedral  :  4.506  19.372   2316
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.13 %
    Favored  : 91.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.17), residues: 2040
  helix:  0.69 (0.12), residues: 1416
  sheet:  None (None), residues: 0
  loop :  0.69 (0.27), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  95 
 TYR   0.018   0.002   TYR J 123 
 PHE   0.027   0.003   PHE H  31 
 TRP   0.007   0.002   TRP L 154 
 HIS   0.005   0.002   HIS F 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (16956)
  covalent geometry    : angle       0.58540 (23016)
  SS BOND              : bond        0.00571 (   12)
  SS BOND              : angle       1.07275 (   24)
  hydrogen bonds       : bond        0.07531 ( 1152)
  hydrogen bonds       : angle       5.81427 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 264
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6495 (tttt) cc_final: 0.5690 (ttpt)
REVERT: B  171 LYS cc_start: 0.6519 (tttt) cc_final: 0.5629 (ttpt)
REVERT: C  162 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7168 (pptt)
REVERT: C  171 LYS cc_start: 0.6545 (tttt) cc_final: 0.5728 (ttpt)
REVERT: D  171 LYS cc_start: 0.6372 (tttt) cc_final: 0.5606 (ttpt)
REVERT: E  171 LYS cc_start: 0.6471 (tttt) cc_final: 0.5670 (ttpt)
REVERT: E  179 SER cc_start: 0.8856 (m) cc_final: 0.8564 (p)
REVERT: F  171 LYS cc_start: 0.6587 (tttt) cc_final: 0.5780 (ttpt)
REVERT: G  171 LYS cc_start: 0.6252 (tttt) cc_final: 0.5146 (tmtt)
REVERT: H  171 LYS cc_start: 0.6295 (tttt) cc_final: 0.5503 (ttpt)
REVERT: H  179 SER cc_start: 0.8800 (m) cc_final: 0.8530 (p)
REVERT: I  171 LYS cc_start: 0.6472 (tttt) cc_final: 0.5355 (pptt)
REVERT: J  171 LYS cc_start: 0.6380 (tttt) cc_final: 0.5337 (tmtt)
REVERT: K  171 LYS cc_start: 0.6439 (tttt) cc_final: 0.5676 (ttpt)
REVERT: L  171 LYS cc_start: 0.6431 (tttt) cc_final: 0.5539 (ttpt)
  outliers start: 19
  outliers final: 9
  residues processed: 267
  average time/residue: 0.8195
  time to fit residues: 238.2487
Evaluate side-chains
  235 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 225
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain D residue  160 THR
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain G residue  160 THR
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain J residue  160 THR
Chi-restraints excluded: chain K residue  160 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 179 optimal weight:    0.9990
   chunk 181 optimal weight:    2.9990
   chunk 152 optimal weight:    0.0270
   chunk 126 optimal weight:    2.9990
   chunk 160 optimal weight:    2.9990
   chunk 195 optimal weight:    4.9990
   chunk 202 optimal weight:    0.0270
   chunk 43 optimal weight:    0.0770
   chunk 107 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.4254

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

Flipped N/Q/H residues before XYZ refinement:
** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.188897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.176489 restraints weight = 49346.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 1.31
r_work: 0.3883 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  16968  Z= 0.144
  Angle     :  0.529   6.869  23040  Z= 0.295
  Chirality :  0.037   0.124   2532
  Planarity :  0.004   0.036   2988
  Dihedral  :  4.268  22.540   2316
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  7.64 %
    Favored  : 91.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.18), residues: 2040
  helix:  1.50 (0.13), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.96 (0.29), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  95 
 TYR   0.015   0.002   TYR D  75 
 PHE   0.025   0.002   PHE H  31 
 TRP   0.013   0.002   TRP C 154 
 HIS   0.005   0.001   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (16956)
  covalent geometry    : angle       0.52880 (23016)
  SS BOND              : bond        0.00554 (   12)
  SS BOND              : angle       0.99200 (   24)
  hydrogen bonds       : bond        0.06568 ( 1152)
  hydrogen bonds       : angle       5.46603 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 247
  time to evaluate  : 0.534 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6367 (tttt) cc_final: 0.5498 (ttpt)
REVERT: A  179 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8514 (p)
REVERT: B  171 LYS cc_start: 0.6392 (tttt) cc_final: 0.5484 (ttpt)
REVERT: C  171 LYS cc_start: 0.6451 (tttt) cc_final: 0.5628 (ttpt)
REVERT: C  179 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8478 (p)
REVERT: D  171 LYS cc_start: 0.6208 (tttt) cc_final: 0.5440 (ttpt)
REVERT: E  171 LYS cc_start: 0.6275 (tttt) cc_final: 0.5458 (ttpt)
REVERT: E  179 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8507 (p)
REVERT: F  171 LYS cc_start: 0.6445 (tttt) cc_final: 0.5462 (pptt)
REVERT: G  171 LYS cc_start: 0.5975 (tttt) cc_final: 0.5134 (ttpt)
REVERT: H  171 LYS cc_start: 0.6239 (tttt) cc_final: 0.5439 (ttpt)
REVERT: H  179 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8490 (p)
REVERT: I  171 LYS cc_start: 0.6330 (tttt) cc_final: 0.5233 (pptt)
REVERT: J  171 LYS cc_start: 0.6337 (tttt) cc_final: 0.5516 (ttpt)
REVERT: K  171 LYS cc_start: 0.6339 (tttt) cc_final: 0.5584 (ttpt)
REVERT: K  179 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8534 (p)
REVERT: L  171 LYS cc_start: 0.6344 (tttt) cc_final: 0.5472 (ttpt)
  outliers start: 21
  outliers final: 10
  residues processed: 250
  average time/residue: 0.8121
  time to fit residues: 221.1302
Evaluate side-chains
  241 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 226
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 177 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 107 ASN
** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.183946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.171448 restraints weight = 49533.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 1.27
r_work: 0.3820 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3653
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3653 r_free = 0.3653    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3653 r_free = 0.3653    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3653
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16968  Z= 0.171
  Angle     :  0.578   6.229  23040  Z= 0.322
  Chirality :  0.039   0.143   2532
  Planarity :  0.005   0.039   2988
  Dihedral  :  4.400  20.716   2316
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  8.28 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.18), residues: 2040
  helix:  1.64 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  1.10 (0.28), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  95 
 TYR   0.019   0.002   TYR A 123 
 PHE   0.019   0.002   PHE H  31 
 TRP   0.017   0.002   TRP C 154 
 HIS   0.007   0.003   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (16956)
  covalent geometry    : angle       0.57769 (23016)
  SS BOND              : bond        0.00646 (   12)
  SS BOND              : angle       1.02544 (   24)
  hydrogen bonds       : bond        0.07362 ( 1152)
  hydrogen bonds       : angle       5.49907 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 252
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6313 (tttt) cc_final: 0.5428 (ttpt)
REVERT: A  179 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8537 (p)
REVERT: B  171 LYS cc_start: 0.6385 (tttt) cc_final: 0.5470 (ttpt)
REVERT: C  171 LYS cc_start: 0.6516 (tttt) cc_final: 0.5623 (ttpt)
REVERT: C  179 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8511 (p)
REVERT: D  171 LYS cc_start: 0.6309 (tttt) cc_final: 0.5494 (ttpt)
REVERT: E  171 LYS cc_start: 0.6200 (tttt) cc_final: 0.5103 (pptt)
REVERT: F  171 LYS cc_start: 0.6440 (tttt) cc_final: 0.5584 (ttpt)
REVERT: G  171 LYS cc_start: 0.6042 (tttt) cc_final: 0.5161 (ttpt)
REVERT: H  125 GLU cc_start: 0.8431 (tt0) cc_final: 0.8188 (tt0)
REVERT: H  171 LYS cc_start: 0.6180 (tttt) cc_final: 0.5408 (ttpt)
REVERT: H  179 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8503 (p)
REVERT: I  171 LYS cc_start: 0.6305 (tttt) cc_final: 0.5373 (ttpt)
REVERT: J  171 LYS cc_start: 0.6354 (tttt) cc_final: 0.5509 (ttpt)
REVERT: K  171 LYS cc_start: 0.6278 (tttt) cc_final: 0.5496 (ttpt)
REVERT: L  171 LYS cc_start: 0.6276 (tttt) cc_final: 0.5336 (ttpt)
  outliers start: 31
  outliers final: 17
  residues processed: 261
  average time/residue: 0.8571
  time to fit residues: 242.6383
Evaluate side-chains
  255 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 235
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue  160 THR
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue  160 THR
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 59 optimal weight:    0.0060
   chunk 145 optimal weight:    0.7980
   chunk 148 optimal weight:    0.9980
   chunk 194 optimal weight:    2.9990
   chunk 158 optimal weight:    0.6980
   chunk 88 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 186 optimal weight:    0.0270
   chunk 56 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.4254

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.189352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.177265 restraints weight = 49564.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 1.24
r_work: 0.3889 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  16968  Z= 0.134
  Angle     :  0.503   7.461  23040  Z= 0.283
  Chirality :  0.036   0.128   2532
  Planarity :  0.004   0.044   2988
  Dihedral  :  4.101  23.528   2316
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.48 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.18), residues: 2040
  helix:  1.92 (0.13), residues: 1452
  sheet:  None (None), residues: 0
  loop :  1.31 (0.28), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  95 
 TYR   0.015   0.001   TYR B 123 
 PHE   0.024   0.002   PHE G  31 
 TRP   0.017   0.002   TRP C 154 
 HIS   0.003   0.001   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (16956)
  covalent geometry    : angle       0.50263 (23016)
  SS BOND              : bond        0.00500 (   12)
  SS BOND              : angle       0.97396 (   24)
  hydrogen bonds       : bond        0.06247 ( 1152)
  hydrogen bonds       : angle       5.28244 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 256
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6255 (tttt) cc_final: 0.5414 (ttpt)
REVERT: A  179 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8511 (p)
REVERT: B  171 LYS cc_start: 0.6194 (tttt) cc_final: 0.5295 (ttpt)
REVERT: C  171 LYS cc_start: 0.6480 (tttt) cc_final: 0.5593 (ttpt)
REVERT: C  179 SER cc_start: 0.8743 (m) cc_final: 0.8479 (p)
REVERT: D  171 LYS cc_start: 0.6191 (tttt) cc_final: 0.5399 (ttpt)
REVERT: E  171 LYS cc_start: 0.6140 (tttt) cc_final: 0.5290 (ttpt)
REVERT: F   41 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8121 (tmm-80)
REVERT: F  125 GLU cc_start: 0.8464 (tt0) cc_final: 0.8262 (tt0)
REVERT: F  171 LYS cc_start: 0.6285 (tttt) cc_final: 0.5482 (ttpt)
REVERT: F  179 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8473 (p)
REVERT: G  171 LYS cc_start: 0.5924 (tttt) cc_final: 0.5054 (ttpt)
REVERT: H  125 GLU cc_start: 0.8342 (tt0) cc_final: 0.8123 (tt0)
REVERT: H  171 LYS cc_start: 0.6102 (tttt) cc_final: 0.5305 (ttpt)
REVERT: H  179 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8471 (p)
REVERT: I  171 LYS cc_start: 0.6358 (tttt) cc_final: 0.5375 (ttpt)
REVERT: J  171 LYS cc_start: 0.6209 (tttt) cc_final: 0.5389 (ttpt)
REVERT: K   54 GLU cc_start: 0.8130 (pm20) cc_final: 0.7815 (pm20)
REVERT: K  171 LYS cc_start: 0.6238 (tttt) cc_final: 0.5455 (ttpt)
REVERT: K  179 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8539 (p)
REVERT: L  171 LYS cc_start: 0.6084 (tttt) cc_final: 0.5195 (ttpt)
  outliers start: 24
  outliers final: 17
  residues processed: 259
  average time/residue: 0.8212
  time to fit residues: 231.1953
Evaluate side-chains
  251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 229
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue   14 ILE
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue   14 ILE
Chi-restraints excluded: chain G residue  160 THR
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue  160 THR
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 176 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 137 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 165 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.184787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.172474 restraints weight = 48455.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 1.27
r_work: 0.3840 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  16968  Z= 0.163
  Angle     :  0.557   5.320  23040  Z= 0.311
  Chirality :  0.038   0.143   2532
  Planarity :  0.005   0.044   2988
  Dihedral  :  4.236  16.015   2316
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.83 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.18), residues: 2040
  helix:  1.88 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  1.28 (0.27), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  95 
 TYR   0.019   0.002   TYR E 123 
 PHE   0.016   0.002   PHE H  31 
 TRP   0.018   0.002   TRP C 154 
 HIS   0.006   0.002   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (16956)
  covalent geometry    : angle       0.55617 (23016)
  SS BOND              : bond        0.00586 (   12)
  SS BOND              : angle       1.03404 (   24)
  hydrogen bonds       : bond        0.07078 ( 1152)
  hydrogen bonds       : angle       5.38047 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 243
  time to evaluate  : 0.618 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6235 (tttt) cc_final: 0.5360 (ttpt)
REVERT: A  179 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8527 (p)
REVERT: B  171 LYS cc_start: 0.6155 (tttt) cc_final: 0.5255 (ttpt)
REVERT: C  171 LYS cc_start: 0.6396 (tttt) cc_final: 0.5511 (ttpt)
REVERT: C  179 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8491 (p)
REVERT: D  171 LYS cc_start: 0.6200 (tttt) cc_final: 0.5409 (ttpt)
REVERT: E  171 LYS cc_start: 0.6163 (tttt) cc_final: 0.5311 (ttpt)
REVERT: F  171 LYS cc_start: 0.6308 (tttt) cc_final: 0.5537 (ttpt)
REVERT: G  171 LYS cc_start: 0.5991 (tttt) cc_final: 0.5119 (ttpt)
REVERT: H  125 GLU cc_start: 0.8348 (tt0) cc_final: 0.8126 (tt0)
REVERT: H  171 LYS cc_start: 0.6152 (tttt) cc_final: 0.5369 (ttpt)
REVERT: H  179 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8473 (p)
REVERT: I  171 LYS cc_start: 0.6347 (tttt) cc_final: 0.5046 (pptt)
REVERT: J  171 LYS cc_start: 0.6221 (tttt) cc_final: 0.5393 (ttpt)
REVERT: K  171 LYS cc_start: 0.6215 (tttt) cc_final: 0.5430 (ttpt)
REVERT: L  171 LYS cc_start: 0.5973 (tttt) cc_final: 0.5148 (ttpt)
  outliers start: 31
  outliers final: 20
  residues processed: 252
  average time/residue: 0.8335
  time to fit residues: 228.6310
Evaluate side-chains
  257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 234
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue   14 ILE
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue   14 ILE
Chi-restraints excluded: chain G residue  160 THR
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue  160 THR
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 115 optimal weight:    8.9990
   chunk 191 optimal weight:    5.9990
   chunk 120 optimal weight:    4.9990
   chunk 202 optimal weight:    0.0970
   chunk 50 optimal weight:    6.9990
   chunk 77 optimal weight:    0.5980
   chunk 163 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.185909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.173535 restraints weight = 50707.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.26
r_work: 0.3840 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  16968  Z= 0.149
  Angle     :  0.531   6.320  23040  Z= 0.299
  Chirality :  0.037   0.137   2532
  Planarity :  0.004   0.043   2988
  Dihedral  :  4.128  14.501   2316
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  9.77 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.18), residues: 2040
  helix:  1.84 (0.13), residues: 1452
  sheet:  None (None), residues: 0
  loop :  1.44 (0.28), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  95 
 TYR   0.018   0.002   TYR A 123 
 PHE   0.019   0.002   PHE B  31 
 TRP   0.021   0.002   TRP C 154 
 HIS   0.005   0.002   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16956)
  covalent geometry    : angle       0.53026 (23016)
  SS BOND              : bond        0.00585 (   12)
  SS BOND              : angle       1.04506 (   24)
  hydrogen bonds       : bond        0.06796 ( 1152)
  hydrogen bonds       : angle       5.32077 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 248
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6212 (tttt) cc_final: 0.5331 (ttpt)
REVERT: A  179 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8549 (p)
REVERT: B  171 LYS cc_start: 0.6035 (tttt) cc_final: 0.5108 (ttpt)
REVERT: C  171 LYS cc_start: 0.6359 (tttt) cc_final: 0.5480 (ttpt)
REVERT: C  179 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8494 (p)
REVERT: D  171 LYS cc_start: 0.6206 (tttt) cc_final: 0.5404 (ttpt)
REVERT: E  171 LYS cc_start: 0.6189 (tttt) cc_final: 0.5322 (ttpt)
REVERT: F   41 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8195 (tmm-80)
REVERT: F  171 LYS cc_start: 0.6436 (tttt) cc_final: 0.5558 (ttpt)
REVERT: F  179 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8495 (p)
REVERT: G  171 LYS cc_start: 0.5916 (tttt) cc_final: 0.5002 (ttpt)
REVERT: H  125 GLU cc_start: 0.8328 (tt0) cc_final: 0.8110 (tt0)
REVERT: H  171 LYS cc_start: 0.6113 (tttt) cc_final: 0.5350 (ttpt)
REVERT: H  179 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8459 (p)
REVERT: I  171 LYS cc_start: 0.6337 (tttt) cc_final: 0.5143 (tmtt)
REVERT: J  171 LYS cc_start: 0.6218 (tttt) cc_final: 0.5392 (ttpt)
REVERT: K   41 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8336 (tmm-80)
REVERT: K  171 LYS cc_start: 0.6234 (tttt) cc_final: 0.5450 (ttpt)
REVERT: L  171 LYS cc_start: 0.5899 (tttt) cc_final: 0.4995 (ttpt)
  outliers start: 33
  outliers final: 25
  residues processed: 260
  average time/residue: 0.8408
  time to fit residues: 237.3032
Evaluate side-chains
  269 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 238
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain D residue   14 ILE
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue   14 ILE
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue   14 ILE
Chi-restraints excluded: chain G residue  160 THR
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue   14 ILE
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue  160 THR
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue   14 ILE
Chi-restraints excluded: chain K residue   41 ARG
Chi-restraints excluded: chain K residue   95 ARG
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 167 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 189 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 190 optimal weight:    0.0040
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.9394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.184323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.170186 restraints weight = 52102.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 1.47
r_work: 0.3804 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3668 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16968  Z= 0.151
  Angle     :  0.539   5.264  23040  Z= 0.303
  Chirality :  0.037   0.137   2532
  Planarity :  0.004   0.042   2988
  Dihedral  :  4.107  14.576   2316
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.52 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.18), residues: 2040
  helix:  1.83 (0.13), residues: 1452
  sheet:  None (None), residues: 0
  loop :  1.47 (0.28), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  95 
 TYR   0.018   0.002   TYR E 123 
 PHE   0.018   0.002   PHE B  31 
 TRP   0.022   0.003   TRP C 154 
 HIS   0.005   0.002   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (16956)
  covalent geometry    : angle       0.53843 (23016)
  SS BOND              : bond        0.00601 (   12)
  SS BOND              : angle       1.06046 (   24)
  hydrogen bonds       : bond        0.06835 ( 1152)
  hydrogen bonds       : angle       5.31551 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 245
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6161 (tttt) cc_final: 0.5245 (ttpt)
REVERT: A  179 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8493 (p)
REVERT: B  171 LYS cc_start: 0.5891 (tttt) cc_final: 0.4947 (ttpt)
REVERT: C  171 LYS cc_start: 0.6320 (tttt) cc_final: 0.5411 (ttpt)
REVERT: C  179 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8481 (p)
REVERT: D  171 LYS cc_start: 0.6158 (tttt) cc_final: 0.5280 (ttpt)
REVERT: E  171 LYS cc_start: 0.6150 (tttt) cc_final: 0.5265 (ttpt)
REVERT: F  171 LYS cc_start: 0.6393 (tttt) cc_final: 0.5117 (pptt)
REVERT: F  179 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8496 (p)
REVERT: G   54 GLU cc_start: 0.8281 (pm20) cc_final: 0.8001 (pm20)
REVERT: G  171 LYS cc_start: 0.5875 (tttt) cc_final: 0.4912 (ttpt)
REVERT: H  125 GLU cc_start: 0.8356 (tt0) cc_final: 0.8129 (tt0)
REVERT: H  171 LYS cc_start: 0.6012 (tttt) cc_final: 0.5221 (ttpt)
REVERT: H  179 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8441 (p)
REVERT: I   41 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8347 (tmm-80)
REVERT: I  171 LYS cc_start: 0.6201 (tttt) cc_final: 0.4938 (pptt)
REVERT: J   95 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7749 (mtp85)
REVERT: J  171 LYS cc_start: 0.6179 (tttt) cc_final: 0.5302 (ttpt)
REVERT: K   41 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8397 (tmm-80)
REVERT: K   54 GLU cc_start: 0.8218 (pm20) cc_final: 0.7894 (pm20)
REVERT: K  171 LYS cc_start: 0.6168 (tttt) cc_final: 0.5328 (ttpt)
REVERT: L  171 LYS cc_start: 0.5882 (tttt) cc_final: 0.4958 (ttpt)
  outliers start: 35
  outliers final: 26
  residues processed: 258
  average time/residue: 0.8401
  time to fit residues: 235.3012
Evaluate side-chains
  272 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 239
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain D residue   14 ILE
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue   14 ILE
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue   14 ILE
Chi-restraints excluded: chain G residue  160 THR
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue   14 ILE
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue   41 ARG
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue   95 ARG
Chi-restraints excluded: chain J residue  160 THR
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue   14 ILE
Chi-restraints excluded: chain K residue   41 ARG
Chi-restraints excluded: chain K residue   95 ARG
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 69 optimal weight:    0.5980
   chunk 98 optimal weight:   10.0000
   chunk 146 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 180 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 145 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.184745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.170979 restraints weight = 46143.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 1.41
r_work: 0.3814 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3678 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16968  Z= 0.147
  Angle     :  0.532   4.884  23040  Z= 0.299
  Chirality :  0.037   0.137   2532
  Planarity :  0.004   0.041   2988
  Dihedral  :  4.063  14.405   2316
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.75 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.18), residues: 2040
  helix:  1.87 (0.13), residues: 1452
  sheet:  None (None), residues: 0
  loop :  1.48 (0.28), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  95 
 TYR   0.017   0.002   TYR E 123 
 PHE   0.018   0.002   PHE B  31 
 TRP   0.024   0.003   TRP C 154 
 HIS   0.005   0.002   HIS H 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (16956)
  covalent geometry    : angle       0.53116 (23016)
  SS BOND              : bond        0.00601 (   12)
  SS BOND              : angle       1.07372 (   24)
  hydrogen bonds       : bond        0.06741 ( 1152)
  hydrogen bonds       : angle       5.28668 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 246
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6127 (tttt) cc_final: 0.5208 (ttpt)
REVERT: A  179 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8502 (p)
REVERT: B  171 LYS cc_start: 0.5893 (tttt) cc_final: 0.4953 (ttpt)
REVERT: C  171 LYS cc_start: 0.6289 (tttt) cc_final: 0.5380 (ttpt)
REVERT: C  179 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8471 (p)
REVERT: D  171 LYS cc_start: 0.6156 (tttt) cc_final: 0.5274 (ttpt)
REVERT: E  171 LYS cc_start: 0.6127 (tttt) cc_final: 0.5236 (ttpt)
REVERT: F  171 LYS cc_start: 0.6317 (tttt) cc_final: 0.5010 (pptt)
REVERT: F  179 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8496 (p)
REVERT: G   54 GLU cc_start: 0.8293 (pm20) cc_final: 0.8007 (pm20)
REVERT: G  171 LYS cc_start: 0.5858 (tttt) cc_final: 0.4888 (ttpt)
REVERT: H  125 GLU cc_start: 0.8350 (tt0) cc_final: 0.8125 (tt0)
REVERT: H  171 LYS cc_start: 0.6074 (tttt) cc_final: 0.5264 (ttpt)
REVERT: H  179 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8440 (p)
REVERT: I   41 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8330 (tmm-80)
REVERT: I  171 LYS cc_start: 0.6150 (tttt) cc_final: 0.4889 (pptt)
REVERT: J   95 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (mtp85)
REVERT: J  171 LYS cc_start: 0.6196 (tttt) cc_final: 0.5311 (ttpt)
REVERT: K   41 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8399 (tmm-80)
REVERT: K  171 LYS cc_start: 0.6184 (tttt) cc_final: 0.5318 (ttpt)
REVERT: L  171 LYS cc_start: 0.5860 (tttt) cc_final: 0.4935 (ttpt)
  outliers start: 34
  outliers final: 24
  residues processed: 259
  average time/residue: 0.8608
  time to fit residues: 241.8891
Evaluate side-chains
  267 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 236
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain D residue   14 ILE
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue  160 THR
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue   14 ILE
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue   41 ARG
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue   95 ARG
Chi-restraints excluded: chain J residue  160 THR
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue   14 ILE
Chi-restraints excluded: chain K residue   41 ARG
Chi-restraints excluded: chain K residue   95 ARG
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue   14 ILE
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 141 optimal weight:    2.9990
   chunk 167 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 174 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 179 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9990
   chunk 172 optimal weight:    0.7980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.185057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.171339 restraints weight = 48815.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 1.44
r_work: 0.3833 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16968  Z= 0.146
  Angle     :  0.532   5.245  23040  Z= 0.299
  Chirality :  0.037   0.134   2532
  Planarity :  0.004   0.041   2988
  Dihedral  :  4.030  14.266   2316
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.15 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.18), residues: 2040
  helix:  1.90 (0.13), residues: 1452
  sheet:  None (None), residues: 0
  loop :  1.50 (0.28), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  95 
 TYR   0.017   0.002   TYR A 123 
 PHE   0.018   0.002   PHE B  31 
 TRP   0.024   0.003   TRP C 154 
 HIS   0.004   0.002   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (16956)
  covalent geometry    : angle       0.53127 (23016)
  SS BOND              : bond        0.00600 (   12)
  SS BOND              : angle       1.07632 (   24)
  hydrogen bonds       : bond        0.06671 ( 1152)
  hydrogen bonds       : angle       5.26135 ( 3372)

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 244
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.6122 (tttt) cc_final: 0.5216 (ttpt)
REVERT: A  179 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8487 (p)
REVERT: B  171 LYS cc_start: 0.5915 (tttt) cc_final: 0.4992 (ttpt)
REVERT: C  171 LYS cc_start: 0.6311 (tttt) cc_final: 0.5418 (ttpt)
REVERT: C  179 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8465 (p)
REVERT: D  171 LYS cc_start: 0.6158 (tttt) cc_final: 0.5277 (ttpt)
REVERT: E  171 LYS cc_start: 0.6112 (tttt) cc_final: 0.5233 (ttpt)
REVERT: F  171 LYS cc_start: 0.6305 (tttt) cc_final: 0.5062 (pptt)
REVERT: F  179 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8490 (p)
REVERT: G   54 GLU cc_start: 0.8169 (pm20) cc_final: 0.7872 (pm20)
REVERT: G  171 LYS cc_start: 0.5823 (tttt) cc_final: 0.4877 (ttpt)
REVERT: H  125 GLU cc_start: 0.8299 (tt0) cc_final: 0.8078 (tt0)
REVERT: H  171 LYS cc_start: 0.6087 (tttt) cc_final: 0.5291 (ttpt)
REVERT: H  179 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8422 (p)
REVERT: I   41 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8268 (tmm-80)
REVERT: I  171 LYS cc_start: 0.6163 (tttt) cc_final: 0.4909 (pptt)
REVERT: J  171 LYS cc_start: 0.6172 (tttt) cc_final: 0.5308 (ttpt)
REVERT: K   41 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8322 (tmm-80)
REVERT: K  171 LYS cc_start: 0.6104 (tttt) cc_final: 0.5269 (ttpt)
REVERT: L  171 LYS cc_start: 0.5899 (tttt) cc_final: 0.5000 (ttpt)
  outliers start: 35
  outliers final: 26
  residues processed: 257
  average time/residue: 0.8866
  time to fit residues: 246.7007
Evaluate side-chains
  264 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 232
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain D residue   14 ILE
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 SER
Chi-restraints excluded: chain G residue  160 THR
Chi-restraints excluded: chain G residue  179 SER
Chi-restraints excluded: chain H residue   14 ILE
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  179 SER
Chi-restraints excluded: chain I residue   14 ILE
Chi-restraints excluded: chain I residue   41 ARG
Chi-restraints excluded: chain I residue  179 SER
Chi-restraints excluded: chain J residue   14 ILE
Chi-restraints excluded: chain J residue  160 THR
Chi-restraints excluded: chain J residue  179 SER
Chi-restraints excluded: chain K residue   14 ILE
Chi-restraints excluded: chain K residue   41 ARG
Chi-restraints excluded: chain K residue   95 ARG
Chi-restraints excluded: chain K residue  179 SER
Chi-restraints excluded: chain L residue  179 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 138 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 165 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 175 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.183159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.169327 restraints weight = 47659.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 1.43
r_work: 0.3795 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3664 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16968  Z= 0.167
  Angle     :  0.569   5.179  23040  Z= 0.318
  Chirality :  0.038   0.138   2532
  Planarity :  0.005   0.045   2988
  Dihedral  :  4.163  14.981   2316
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.92 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.18), residues: 2040
  helix:  1.86 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  1.40 (0.26), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  95 
 TYR   0.020   0.002   TYR E 123 
 PHE   0.015   0.002   PHE B  31 
 TRP   0.023   0.003   TRP C 154 
 HIS   0.006   0.002   HIS C 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (16956)
  covalent geometry    : angle       0.56816 (23016)
  SS BOND              : bond        0.00655 (   12)
  SS BOND              : angle       1.09445 (   24)
  hydrogen bonds       : bond        0.07179 ( 1152)
  hydrogen bonds       : angle       5.34583 ( 3372)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7095.46 seconds
wall clock time: 121 minutes 18.45 seconds (7278.45 seconds total)