Starting phenix.real_space_refine
on Wed Sep 17 21:27:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nh4_49400/09_2025/9nh4_49400_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nh4_49400/09_2025/9nh4_49400.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nh4_49400/09_2025/9nh4_49400.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nh4_49400/09_2025/9nh4_49400.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nh4_49400/09_2025/9nh4_49400_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nh4_49400/09_2025/9nh4_49400_neut.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    7390      2.51       5
     N    1865      2.21       5
     O    2045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  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: 11320
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2260
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
    Chain: "B"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2260
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
    Chain: "C"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2260
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
    Chain: "D"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2260
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
    Chain: "E"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2260
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.83, per 1000 atoms: 0.25
  Number of scatterers: 11320
  At special positions: 0
  Unit cell: (89.984, 89.984, 110.112, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    2045      8.00
     N    1865      7.00
     C    7390      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 520.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2620

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 20 sheets defined
      28.0% alpha, 43.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.874A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 224
      removed outlier: 3.577A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 244
    Processing helix  chain 'A' and resid 261 through 285
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.873A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 224
      removed outlier: 3.578A  pdb=" N   LEU B 212 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 244
    Processing helix  chain 'B' and resid 261 through 285
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.873A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 224
      removed outlier: 3.578A  pdb=" N   LEU C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 244
    Processing helix  chain 'C' and resid 261 through 285
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.874A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 224
      removed outlier: 3.576A  pdb=" N   LEU D 212 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 244
    Processing helix  chain 'D' and resid 261 through 285
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.874A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 224
      removed outlier: 3.578A  pdb=" N   LEU E 212 " --> pdb=" O   PHE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 244
    Processing helix  chain 'E' and resid 261 through 285
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.620A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE A 101 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.620A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE A 101 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU A 128 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE A 157 " --> pdb=" O   TRP A 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU A 128 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58
      removed outlier: 3.621A  pdb=" N   VAL B  58 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE B 101 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58
      removed outlier: 3.621A  pdb=" N   VAL B  58 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE B 101 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU B 128 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL B 193 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 160 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU B 128 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL B 193 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58
      removed outlier: 3.621A  pdb=" N   VAL C  58 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE C 101 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58
      removed outlier: 3.621A  pdb=" N   VAL C  58 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE C 101 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU C 128 " --> pdb=" O   VAL C 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL C 193 " --> pdb=" O   LEU C 128 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 160 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU C 128 " --> pdb=" O   VAL C 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL C 193 " --> pdb=" O   LEU C 128 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58
      removed outlier: 3.620A  pdb=" N   VAL D  58 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE D 101 " --> pdb=" O   MET D  93 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58
      removed outlier: 3.620A  pdb=" N   VAL D  58 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE D 101 " --> pdb=" O   MET D  93 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU D 128 " --> pdb=" O   VAL D 193 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL D 193 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE D 157 " --> pdb=" O   TRP D 160 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78
      removed outlier: 3.640A  pdb=" N   LEU D 128 " --> pdb=" O   VAL D 193 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL D 193 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58
      removed outlier: 3.620A  pdb=" N   VAL E  58 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE E 101 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58
      removed outlier: 3.620A  pdb=" N   VAL E  58 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE E 101 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 3.639A  pdb=" N   LEU E 128 " --> pdb=" O   VAL E 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL E 193 " --> pdb=" O   LEU E 128 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE E 157 " --> pdb=" O   TRP E 160 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 3.639A  pdb=" N   LEU E 128 " --> pdb=" O   VAL E 193 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL E 193 " --> pdb=" O   LEU E 128 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    565 hydrogen bonds defined for protein.
    1620 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: 1.93

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3544
        1.34 -     1.46: 2246
        1.46 -     1.57: 5805
        1.57 -     1.69: 5
        1.69 -     1.80: 40
  Bond restraints: 11640
  Sorted by residual:
  bond pdb=" N   LEU E 210 "
       pdb=" CA  LEU E 210 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 8.50e-03 1.38e+04 1.04e+01
  bond pdb=" N   ILE C 157 "
       pdb=" CA  ILE C 157 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 1.02e+01
  bond pdb=" N   ILE B 157 "
       pdb=" CA  ILE B 157 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 1.01e+01
  bond pdb=" N   ILE D 157 "
       pdb=" CA  ILE D 157 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 1.00e+01
  bond pdb=" N   ILE A 157 "
       pdb=" CA  ILE A 157 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 9.92e+00
  ... (remaining 11635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 14922
        1.72 -     3.44: 795
        3.44 -     5.16: 95
        5.16 -     6.88: 28
        6.88 -     8.60: 25
  Bond angle restraints: 15865
  Sorted by residual:
  angle pdb=" N   LEU E 210 "
        pdb=" CA  LEU E 210 "
        pdb=" CB  LEU E 210 "
      ideal   model   delta    sigma   weight residual
     110.42  115.36   -4.94 1.18e+00 7.18e-01 1.75e+01
  angle pdb=" N   GLU D 159 "
        pdb=" CA  GLU D 159 "
        pdb=" C   GLU D 159 "
      ideal   model   delta    sigma   weight residual
     112.92  108.11    4.81 1.23e+00 6.61e-01 1.53e+01
  angle pdb=" C   ASN C  60 "
        pdb=" N   THR C  61 "
        pdb=" CA  THR C  61 "
      ideal   model   delta    sigma   weight residual
     121.54  128.98   -7.44 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" C   ASN B  60 "
        pdb=" N   THR B  61 "
        pdb=" CA  THR B  61 "
      ideal   model   delta    sigma   weight residual
     121.54  128.97   -7.43 1.91e+00 2.74e-01 1.51e+01
  angle pdb=" N   GLU B 159 "
        pdb=" CA  GLU B 159 "
        pdb=" C   GLU B 159 "
      ideal   model   delta    sigma   weight residual
     112.92  108.14    4.78 1.23e+00 6.61e-01 1.51e+01
  ... (remaining 15860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.64: 5949
       15.64 -    31.28: 655
       31.28 -    46.92: 141
       46.92 -    62.56: 25
       62.56 -    78.20: 10
  Dihedral angle restraints: 6780
    sinusoidal: 2725
      harmonic: 4055
  Sorted by residual:
  dihedral pdb=" CA  ASP C 113 "
           pdb=" C   ASP C 113 "
           pdb=" N   MET C 114 "
           pdb=" CA  MET C 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.49   18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASP A 113 "
           pdb=" C   ASP A 113 "
           pdb=" N   MET A 114 "
           pdb=" CA  MET A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.50   18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASP D 113 "
           pdb=" C   ASP D 113 "
           pdb=" N   MET D 114 "
           pdb=" CA  MET D 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.51   18.49     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 6777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1119
       0.045 -    0.091: 384
       0.091 -    0.136: 165
       0.136 -    0.181: 57
       0.181 -    0.226: 20
  Chirality restraints: 1745
  Sorted by residual:
  chirality pdb=" CA  LEU E 210 "
            pdb=" N   LEU E 210 "
            pdb=" C   LEU E 210 "
            pdb=" CB  LEU E 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  LEU C 210 "
            pdb=" N   LEU C 210 "
            pdb=" C   LEU C 210 "
            pdb=" CB  LEU C 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  LEU A 210 "
            pdb=" N   LEU A 210 "
            pdb=" C   LEU A 210 "
            pdb=" CB  LEU A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 1742 not shown)

  Planarity restraints: 2015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  50 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO D  51 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO D  51 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D  51 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  50 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO C  51 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C  51 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  51 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  50 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO A  51 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  51 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  51 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2012 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1325
        2.75 -     3.29: 11169
        3.29 -     3.83: 18949
        3.83 -     4.36: 21394
        4.36 -     4.90: 37055
  Nonbonded interactions: 89892
  Sorted by model distance:
  nonbonded pdb=" CD1 TYR A 248 "
            pdb=" CE1 PHE E 247 "
     model   vdw
     2.216 3.640
  nonbonded pdb=" OE2 GLU B  77 "
            pdb=" OH  TYR C  38 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NE2 HIS C 284 "
            pdb=" OE1 GLU D 226 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OE2 GLU C  77 "
            pdb=" OH  TYR D  38 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OE2 GLU A  77 "
            pdb=" OH  TYR B  38 "
     model   vdw
     2.264 3.040
  ... (remaining 89887 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  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:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.920
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
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      :  0.005   0.064  11640  Z= 0.266
  Angle     :  0.887   8.600  15865  Z= 0.492
  Chirality :  0.060   0.226   1745
  Planarity :  0.006   0.041   2015
  Dihedral  : 13.841  78.200   4160
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 20.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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: -2.37 (0.21), residues: 1365
  helix: -0.86 (0.23), residues: 395
  sheet: -1.16 (0.29), residues: 330
  loop : -2.24 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 199 
 TYR   0.019   0.002   TYR B 248 
 PHE   0.015   0.002   PHE C 188 
 TRP   0.013   0.001   TRP B  72 
 HIS   0.011   0.003   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (11640)
  covalent geometry    : angle       0.88681 (15865)
  hydrogen bonds       : bond        0.17140 (  495)
  hydrogen bonds       : angle       8.15833 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.7804 (tpp) cc_final: 0.7600 (mmt)
REVERT: A  123 ARG cc_start: 0.6669 (ptp-110) cc_final: 0.6403 (ptp-170)
REVERT: A  148 TYR cc_start: 0.6383 (m-10) cc_final: 0.6180 (m-10)
REVERT: B   94 LEU cc_start: 0.8599 (mt) cc_final: 0.8314 (mt)
REVERT: B  186 ASN cc_start: 0.8024 (p0) cc_final: 0.7238 (p0)
REVERT: C  186 ASN cc_start: 0.8149 (p0) cc_final: 0.7393 (p0)
REVERT: D   84 SER cc_start: 0.6561 (t) cc_final: 0.6329 (t)
REVERT: D  176 ASP cc_start: 0.6551 (t0) cc_final: 0.6330 (t0)
REVERT: D  180 SER cc_start: 0.6103 (p) cc_final: 0.5659 (m)
REVERT: D  199 ARG cc_start: 0.6809 (ttm110) cc_final: 0.6587 (ttm-80)
REVERT: E  186 ASN cc_start: 0.7982 (p0) cc_final: 0.7411 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.1198
  time to fit residues: 40.6454
Evaluate side-chains
  183 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN
B 251 ASN
C 251 ASN
D 151 ASN
D 177 HIS
D 182 GLN
** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.157742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.139139 restraints weight = 12620.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.138081 restraints weight = 17380.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.138492 restraints weight = 16484.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.137210 restraints weight = 10334.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.137669 restraints weight = 10284.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11640  Z= 0.145
  Angle     :  0.650  11.428  15865  Z= 0.326
  Chirality :  0.047   0.159   1745
  Planarity :  0.004   0.045   2015
  Dihedral  :  5.203  27.859   1515
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.61 %
    Favored  : 86.10 %
  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: -1.78 (0.23), residues: 1365
  helix:  0.26 (0.25), residues: 390
  sheet: -0.95 (0.26), residues: 390
  loop : -2.34 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  99 
 TYR   0.023   0.001   TYR D 248 
 PHE   0.017   0.002   PHE C 236 
 TRP   0.016   0.001   TRP E 224 
 HIS   0.006   0.002   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11640)
  covalent geometry    : angle       0.64972 (15865)
  hydrogen bonds       : bond        0.03879 (  495)
  hydrogen bonds       : angle       5.55408 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 209
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 TYR cc_start: 0.6864 (m-10) cc_final: 0.6600 (m-10)
REVERT: A  151 ASN cc_start: 0.8165 (t0) cc_final: 0.7794 (t0)
REVERT: A  219 SER cc_start: 0.8482 (m) cc_final: 0.7729 (p)
REVERT: B  134 SER cc_start: 0.8263 (m) cc_final: 0.8028 (m)
REVERT: B  144 ASP cc_start: 0.7938 (p0) cc_final: 0.7666 (p0)
REVERT: B  186 ASN cc_start: 0.8036 (p0) cc_final: 0.7574 (p0)
REVERT: B  231 ARG cc_start: 0.5219 (mtm180) cc_final: 0.4832 (mtt180)
REVERT: C   91 ARG cc_start: 0.8595 (ptm-80) cc_final: 0.8229 (ptt-90)
REVERT: C  151 ASN cc_start: 0.8143 (t0) cc_final: 0.7929 (t0)
REVERT: C  173 ILE cc_start: 0.8609 (mm) cc_final: 0.8376 (tt)
REVERT: C  186 ASN cc_start: 0.8155 (p0) cc_final: 0.7463 (p0)
REVERT: D  180 SER cc_start: 0.6410 (p) cc_final: 0.6080 (m)
REVERT: D  186 ASN cc_start: 0.7212 (p0) cc_final: 0.6792 (p0)
REVERT: E   13 ASP cc_start: 0.7653 (p0) cc_final: 0.7345 (p0)
REVERT: E  186 ASN cc_start: 0.8007 (p0) cc_final: 0.7219 (p0)
  outliers start: 16
  outliers final: 6
  residues processed: 218
  average time/residue: 0.1188
  time to fit residues: 36.4123
Evaluate side-chains
  182 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 176
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  249 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 121 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
B  60 ASN
B 182 GLN
D  31 GLN
E 251 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.157518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.129840 restraints weight = 12639.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.131751 restraints weight = 9081.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.133177 restraints weight = 7187.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.133846 restraints weight = 6132.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.133958 restraints weight = 5545.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11640  Z= 0.124
  Angle     :  0.593  10.454  15865  Z= 0.296
  Chirality :  0.046   0.146   1745
  Planarity :  0.003   0.033   2015
  Dihedral  :  4.930  28.414   1515
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.50 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.23), residues: 1365
  helix:  0.69 (0.26), residues: 400
  sheet: -0.58 (0.26), residues: 410
  loop : -2.35 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  99 
 TYR   0.020   0.001   TYR E 248 
 PHE   0.012   0.001   PHE D  95 
 TRP   0.007   0.001   TRP D 224 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11640)
  covalent geometry    : angle       0.59292 (15865)
  hydrogen bonds       : bond        0.03423 (  495)
  hydrogen bonds       : angle       5.06451 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 ARG cc_start: 0.8597 (tpp80) cc_final: 0.7940 (mmt180)
REVERT: A  148 TYR cc_start: 0.6834 (m-10) cc_final: 0.6574 (m-10)
REVERT: A  151 ASN cc_start: 0.8127 (t0) cc_final: 0.7817 (t0)
REVERT: A  219 SER cc_start: 0.8421 (m) cc_final: 0.7738 (p)
REVERT: A  236 PHE cc_start: 0.7487 (m-80) cc_final: 0.7275 (m-10)
REVERT: B  134 SER cc_start: 0.8052 (m) cc_final: 0.7716 (m)
REVERT: B  231 ARG cc_start: 0.5685 (mtm180) cc_final: 0.5266 (mtt180)
REVERT: C   91 ARG cc_start: 0.8874 (ptm-80) cc_final: 0.8085 (ptt-90)
REVERT: C  151 ASN cc_start: 0.8155 (t0) cc_final: 0.7862 (t0)
REVERT: C  186 ASN cc_start: 0.8068 (p0) cc_final: 0.7281 (p0)
REVERT: E   13 ASP cc_start: 0.7576 (p0) cc_final: 0.7317 (p0)
REVERT: E  186 ASN cc_start: 0.8040 (p0) cc_final: 0.7093 (p0)
REVERT: E  239 MET cc_start: 0.7239 (mtt) cc_final: 0.6945 (mtt)
  outliers start: 21
  outliers final: 12
  residues processed: 211
  average time/residue: 0.1215
  time to fit residues: 35.7118
Evaluate side-chains
  182 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 ASN
B 169 HIS
D 151 ASN
D 169 HIS
D 182 GLN
E 169 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.144134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.114577 restraints weight = 12735.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.116197 restraints weight = 10066.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.117156 restraints weight = 8321.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.117894 restraints weight = 7308.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.118184 restraints weight = 6831.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  11640  Z= 0.270
  Angle     :  0.712  10.882  15865  Z= 0.364
  Chirality :  0.050   0.222   1745
  Planarity :  0.004   0.050   2015
  Dihedral  :  5.530  29.457   1515
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.83 %
    Favored  : 79.04 %
  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: -1.56 (0.23), residues: 1365
  helix:  0.71 (0.25), residues: 400
  sheet: -0.83 (0.26), residues: 395
  loop : -2.48 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  99 
 TYR   0.022   0.002   TYR A 204 
 PHE   0.019   0.002   PHE E 119 
 TRP   0.015   0.002   TRP D 224 
 HIS   0.008   0.002   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 (11640)
  covalent geometry    : angle       0.71165 (15865)
  hydrogen bonds       : bond        0.03811 (  495)
  hydrogen bonds       : angle       5.17540 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 202
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7477 (tp-100) cc_final: 0.7089 (tp40)
REVERT: A   34 LYS cc_start: 0.8856 (mttm) cc_final: 0.8513 (mttp)
REVERT: A  117 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8180 (mmt180)
REVERT: A  148 TYR cc_start: 0.7675 (m-10) cc_final: 0.7423 (m-10)
REVERT: A  240 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7757 (tp)
REVERT: B   31 GLN cc_start: 0.7116 (tp-100) cc_final: 0.6822 (tp40)
REVERT: B  117 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8156 (mmt180)
REVERT: B  148 TYR cc_start: 0.7658 (m-10) cc_final: 0.7277 (m-10)
REVERT: B  151 ASN cc_start: 0.8351 (t0) cc_final: 0.8029 (t0)
REVERT: B  199 ARG cc_start: 0.8831 (ttm110) cc_final: 0.7781 (ttm110)
REVERT: C  199 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.7736 (ttm110)
REVERT: C  231 ARG cc_start: 0.5340 (mtm180) cc_final: 0.4843 (mtt180)
REVERT: C  239 MET cc_start: 0.7290 (mtt) cc_final: 0.6946 (mtt)
REVERT: D   13 ASP cc_start: 0.7700 (p0) cc_final: 0.7393 (p0)
REVERT: D   97 ASP cc_start: 0.6077 (p0) cc_final: 0.5808 (p0)
REVERT: D  143 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8316 (t)
REVERT: E   13 ASP cc_start: 0.7628 (p0) cc_final: 0.7296 (p0)
REVERT: E   34 LYS cc_start: 0.8890 (mttm) cc_final: 0.8623 (mttp)
  outliers start: 39
  outliers final: 18
  residues processed: 234
  average time/residue: 0.1231
  time to fit residues: 40.3604
Evaluate side-chains
  203 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 117 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 110 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 133 optimal weight:    0.0060
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.3802

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A 169 HIS
A 182 GLN
B 169 HIS
B 182 GLN
C 169 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.149493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.121477 restraints weight = 12302.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.121530 restraints weight = 9125.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.121530 restraints weight = 8906.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.121530 restraints weight = 8906.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.121530 restraints weight = 8906.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11640  Z= 0.151
  Angle     :  0.618  10.693  15865  Z= 0.307
  Chirality :  0.047   0.168   1745
  Planarity :  0.003   0.030   2015
  Dihedral  :  5.085  25.717   1515
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.12 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.46 (0.23), residues: 1365
  helix:  0.99 (0.25), residues: 395
  sheet: -0.89 (0.26), residues: 395
  loop : -2.46 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  99 
 TYR   0.013   0.001   TYR C 248 
 PHE   0.022   0.001   PHE C 119 
 TRP   0.009   0.001   TRP D 224 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (11640)
  covalent geometry    : angle       0.61824 (15865)
  hydrogen bonds       : bond        0.03320 (  495)
  hydrogen bonds       : angle       4.90946 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 205
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8772 (mttm) cc_final: 0.8513 (mttp)
REVERT: A  151 ASN cc_start: 0.8219 (t0) cc_final: 0.7705 (t0)
REVERT: B  117 ARG cc_start: 0.8702 (tpp80) cc_final: 0.8164 (mmt180)
REVERT: B  148 TYR cc_start: 0.7455 (m-10) cc_final: 0.7124 (m-10)
REVERT: B  151 ASN cc_start: 0.8437 (t0) cc_final: 0.8100 (t0)
REVERT: C  186 ASN cc_start: 0.8066 (p0) cc_final: 0.7125 (p0)
REVERT: C  231 ARG cc_start: 0.4958 (mtm180) cc_final: 0.4641 (mtt180)
REVERT: D   13 ASP cc_start: 0.7626 (p0) cc_final: 0.7405 (p0)
REVERT: D   97 ASP cc_start: 0.6083 (p0) cc_final: 0.5548 (p0)
REVERT: E   13 ASP cc_start: 0.7630 (p0) cc_final: 0.7297 (p0)
REVERT: E   86 ASP cc_start: 0.7880 (p0) cc_final: 0.7677 (p0)
REVERT: E  239 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7137 (mtt)
  outliers start: 33
  outliers final: 16
  residues processed: 228
  average time/residue: 0.1160
  time to fit residues: 37.2460
Evaluate side-chains
  197 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 180
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  239 MET
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  267 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 129 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A  60 ASN
A 169 HIS
B 169 HIS
C 169 HIS
** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 169 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.143718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.115043 restraints weight = 12681.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.116080 restraints weight = 10146.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.116718 restraints weight = 8599.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.117026 restraints weight = 7725.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.117348 restraints weight = 7401.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.5033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11640  Z= 0.229
  Angle     :  0.673  11.270  15865  Z= 0.339
  Chirality :  0.048   0.199   1745
  Planarity :  0.004   0.031   2015
  Dihedral  :  5.318  27.978   1515
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.52 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.53 (0.23), residues: 1365
  helix:  1.03 (0.26), residues: 395
  sheet: -1.03 (0.26), residues: 395
  loop : -2.50 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  99 
 TYR   0.014   0.002   TYR B 248 
 PHE   0.030   0.002   PHE B 119 
 TRP   0.012   0.001   TRP D 224 
 HIS   0.006   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (11640)
  covalent geometry    : angle       0.67333 (15865)
  hydrogen bonds       : bond        0.03588 (  495)
  hydrogen bonds       : angle       5.02428 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 201
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8816 (mttm) cc_final: 0.8538 (mttp)
REVERT: A  151 ASN cc_start: 0.8159 (t0) cc_final: 0.7679 (t0)
REVERT: A  239 MET cc_start: 0.6934 (mtt) cc_final: 0.6715 (mtt)
REVERT: B  117 ARG cc_start: 0.8710 (tpp80) cc_final: 0.8257 (mmt180)
REVERT: B  199 ARG cc_start: 0.8896 (ttm110) cc_final: 0.7896 (ttm110)
REVERT: C   38 TYR cc_start: 0.8664 (m-10) cc_final: 0.8407 (m-10)
REVERT: C  151 ASN cc_start: 0.8235 (t0) cc_final: 0.7855 (t0)
REVERT: C  199 ARG cc_start: 0.8755 (ttm110) cc_final: 0.7801 (ttm110)
REVERT: C  219 SER cc_start: 0.8358 (m) cc_final: 0.7880 (p)
REVERT: D   13 ASP cc_start: 0.7695 (p0) cc_final: 0.7471 (p0)
REVERT: D   97 ASP cc_start: 0.6047 (p0) cc_final: 0.5798 (p0)
REVERT: D  176 ASP cc_start: 0.7507 (t0) cc_final: 0.7283 (t0)
REVERT: D  255 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7210 (mtt180)
REVERT: E   13 ASP cc_start: 0.7628 (p0) cc_final: 0.7323 (p0)
REVERT: E   34 LYS cc_start: 0.8857 (mttm) cc_final: 0.8604 (mttp)
REVERT: E  117 ARG cc_start: 0.8923 (tpp80) cc_final: 0.8173 (mmt180)
REVERT: E  239 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7166 (mtt)
  outliers start: 48
  outliers final: 27
  residues processed: 238
  average time/residue: 0.1215
  time to fit residues: 40.2739
Evaluate side-chains
  222 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  267 ILE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  255 ARG
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  239 MET
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 118 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 114 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 127 optimal weight:    0.6980
   chunk 123 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A 169 HIS
C 169 HIS
D 124 GLN
E 169 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.148225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.119605 restraints weight = 12391.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.121049 restraints weight = 9934.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.121886 restraints weight = 8116.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.122056 restraints weight = 7161.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.122420 restraints weight = 7002.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11640  Z= 0.137
  Angle     :  0.617  11.418  15865  Z= 0.305
  Chirality :  0.046   0.173   1745
  Planarity :  0.003   0.031   2015
  Dihedral  :  4.961  27.156   1515
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.56 %
    Favored  : 76.39 %
  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: -1.39 (0.23), residues: 1365
  helix:  1.18 (0.26), residues: 395
  sheet: -0.95 (0.26), residues: 395
  loop : -2.43 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  99 
 TYR   0.010   0.001   TYR C 248 
 PHE   0.021   0.001   PHE B 119 
 TRP   0.005   0.001   TRP D 224 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11640)
  covalent geometry    : angle       0.61655 (15865)
  hydrogen bonds       : bond        0.03203 (  495)
  hydrogen bonds       : angle       4.81879 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 201
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8752 (mttm) cc_final: 0.8507 (mttp)
REVERT: A  114 MET cc_start: 0.8918 (ttm) cc_final: 0.8684 (ttm)
REVERT: A  151 ASN cc_start: 0.8188 (t0) cc_final: 0.7654 (t0)
REVERT: A  239 MET cc_start: 0.7007 (mtt) cc_final: 0.6761 (mtt)
REVERT: B  117 ARG cc_start: 0.8706 (tpp80) cc_final: 0.8188 (mmt180)
REVERT: B  148 TYR cc_start: 0.7796 (m-10) cc_final: 0.7323 (m-10)
REVERT: B  151 ASN cc_start: 0.8349 (t0) cc_final: 0.8003 (t0)
REVERT: C   86 ASP cc_start: 0.8212 (p0) cc_final: 0.8009 (p0)
REVERT: C  107 LEU cc_start: 0.8751 (tp) cc_final: 0.8526 (tt)
REVERT: C  186 ASN cc_start: 0.8002 (p0) cc_final: 0.7010 (p0)
REVERT: C  199 ARG cc_start: 0.8696 (ttm110) cc_final: 0.7946 (ttm110)
REVERT: C  219 SER cc_start: 0.8320 (m) cc_final: 0.7858 (p)
REVERT: D   13 ASP cc_start: 0.7733 (p0) cc_final: 0.7463 (p0)
REVERT: D   97 ASP cc_start: 0.6101 (p0) cc_final: 0.5808 (p0)
REVERT: D  182 GLN cc_start: 0.7934 (mt0) cc_final: 0.7661 (mt0)
REVERT: E  239 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7116 (mtt)
  outliers start: 38
  outliers final: 25
  residues processed: 230
  average time/residue: 0.1165
  time to fit residues: 37.6812
Evaluate side-chains
  213 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  261 VAL
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  239 MET
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  267 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 86 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 126 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A 169 HIS
C 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.146816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.120842 restraints weight = 12473.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.116654 restraints weight = 15333.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.118570 restraints weight = 11555.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.120427 restraints weight = 9153.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.120882 restraints weight = 7523.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.5275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  11640  Z= 0.163
  Angle     :  0.633  11.639  15865  Z= 0.313
  Chirality :  0.047   0.185   1745
  Planarity :  0.003   0.031   2015
  Dihedral  :  4.997  26.509   1515
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.56 %
    Favored  : 76.47 %
  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: -1.38 (0.23), residues: 1365
  helix:  1.25 (0.26), residues: 395
  sheet: -0.98 (0.26), residues: 395
  loop : -2.46 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  99 
 TYR   0.011   0.001   TYR C 248 
 PHE   0.019   0.001   PHE C 119 
 TRP   0.007   0.001   TRP D 224 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (11640)
  covalent geometry    : angle       0.63279 (15865)
  hydrogen bonds       : bond        0.03262 (  495)
  hydrogen bonds       : angle       4.80059 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 201
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8734 (mttm) cc_final: 0.8480 (mttp)
REVERT: A  151 ASN cc_start: 0.8141 (t0) cc_final: 0.7618 (t0)
REVERT: A  239 MET cc_start: 0.7024 (mtt) cc_final: 0.6767 (mtt)
REVERT: B  117 ARG cc_start: 0.8695 (tpp80) cc_final: 0.8122 (mmt180)
REVERT: B  148 TYR cc_start: 0.7882 (m-10) cc_final: 0.7395 (m-10)
REVERT: B  151 ASN cc_start: 0.8408 (t0) cc_final: 0.8081 (t0)
REVERT: B  199 ARG cc_start: 0.8959 (ttm110) cc_final: 0.8649 (ttm-80)
REVERT: C   80 ASN cc_start: 0.8543 (p0) cc_final: 0.7980 (p0)
REVERT: C  199 ARG cc_start: 0.8730 (ttm110) cc_final: 0.7549 (ttm110)
REVERT: D   13 ASP cc_start: 0.7714 (p0) cc_final: 0.7490 (p0)
REVERT: E  239 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7136 (mtt)
  outliers start: 37
  outliers final: 30
  residues processed: 229
  average time/residue: 0.1144
  time to fit residues: 37.1522
Evaluate side-chains
  224 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 193
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  261 VAL
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue  127 VAL
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  239 MET
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  267 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 114 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 108 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A 169 HIS
A 185 GLN
B  31 GLN
B 186 ASN
C 169 HIS
D 124 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.150104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.121656 restraints weight = 12321.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.123058 restraints weight = 9694.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.124103 restraints weight = 8026.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.124467 restraints weight = 7052.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.124958 restraints weight = 6596.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  11640  Z= 0.123
  Angle     :  0.611  11.451  15865  Z= 0.300
  Chirality :  0.046   0.179   1745
  Planarity :  0.003   0.031   2015
  Dihedral  :  4.819  27.176   1515
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.69 %
    Favored  : 76.06 %
  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: -1.28 (0.23), residues: 1365
  helix:  1.29 (0.26), residues: 395
  sheet: -0.84 (0.25), residues: 395
  loop : -2.43 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  99 
 TYR   0.011   0.001   TYR C 248 
 PHE   0.013   0.001   PHE D 119 
 TRP   0.006   0.001   TRP D 220 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (11640)
  covalent geometry    : angle       0.61118 (15865)
  hydrogen bonds       : bond        0.03075 (  495)
  hydrogen bonds       : angle       4.68207 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASN cc_start: 0.8077 (t0) cc_final: 0.7600 (t0)
REVERT: A  239 MET cc_start: 0.7002 (mtt) cc_final: 0.6768 (mtt)
REVERT: B  117 ARG cc_start: 0.8685 (tpp80) cc_final: 0.8060 (mmt180)
REVERT: B  148 TYR cc_start: 0.7792 (m-10) cc_final: 0.7306 (m-10)
REVERT: B  151 ASN cc_start: 0.8299 (t0) cc_final: 0.7967 (t0)
REVERT: C   80 ASN cc_start: 0.8497 (p0) cc_final: 0.7881 (p0)
REVERT: C  199 ARG cc_start: 0.8647 (ttm110) cc_final: 0.7643 (ttm110)
REVERT: D   13 ASP cc_start: 0.7682 (p0) cc_final: 0.7469 (p0)
REVERT: D  182 GLN cc_start: 0.8028 (mt0) cc_final: 0.7750 (mt0)
REVERT: D  255 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7367 (mtm180)
REVERT: E   97 ASP cc_start: 0.5768 (p0) cc_final: 0.5332 (p0)
REVERT: E   99 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7925 (mtm-85)
  outliers start: 28
  outliers final: 24
  residues processed: 211
  average time/residue: 0.1237
  time to fit residues: 36.1838
Evaluate side-chains
  210 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  261 VAL
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain D residue  255 ARG
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  267 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
C  31 GLN
C 169 HIS
D 182 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.149493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.122804 restraints weight = 12567.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.120408 restraints weight = 14919.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.122783 restraints weight = 13002.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.122953 restraints weight = 9839.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.123075 restraints weight = 8523.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.5347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.208  11640  Z= 0.185
  Angle     :  0.918  59.199  15865  Z= 0.511
  Chirality :  0.046   0.160   1745
  Planarity :  0.004   0.137   2015
  Dihedral  :  4.836  27.147   1515
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.45 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.29 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.15 %
  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: -1.35 (0.23), residues: 1365
  helix:  1.29 (0.25), residues: 395
  sheet: -0.88 (0.26), residues: 375
  loop : -2.48 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D  99 
 TYR   0.010   0.001   TYR C 248 
 PHE   0.023   0.001   PHE B 119 
 TRP   0.010   0.001   TRP D 160 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (11640)
  covalent geometry    : angle       0.91777 (15865)
  hydrogen bonds       : bond        0.03089 (  495)
  hydrogen bonds       : angle       4.67499 ( 1620)

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

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

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2730 Ramachandran restraints generated.
    1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 182
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASN cc_start: 0.8077 (t0) cc_final: 0.7591 (t0)
REVERT: A  239 MET cc_start: 0.6996 (mtt) cc_final: 0.6782 (mtt)
REVERT: B  117 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8075 (mmt180)
REVERT: B  148 TYR cc_start: 0.7798 (m-10) cc_final: 0.7289 (m-10)
REVERT: B  151 ASN cc_start: 0.8293 (t0) cc_final: 0.7968 (t0)
REVERT: C   80 ASN cc_start: 0.8430 (p0) cc_final: 0.7860 (p0)
REVERT: C  199 ARG cc_start: 0.8626 (ttm110) cc_final: 0.7667 (ttm110)
REVERT: D   13 ASP cc_start: 0.7683 (p0) cc_final: 0.7470 (p0)
REVERT: D  255 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7344 (mtm180)
  outliers start: 35
  outliers final: 30
  residues processed: 206
  average time/residue: 0.1240
  time to fit residues: 35.5083
Evaluate side-chains
  213 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 182
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  261 VAL
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  255 ARG
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  261 VAL
Chi-restraints excluded: chain E residue  267 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 169 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.149278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 105)---------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.121779 restraints weight = 12585.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.123372 restraints weight = 9935.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.124474 restraints weight = 7975.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.124839 restraints weight = 7012.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.124863 restraints weight = 6432.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.5352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.208  11640  Z= 0.185
  Angle     :  0.918  59.199  15865  Z= 0.511
  Chirality :  0.046   0.160   1745
  Planarity :  0.004   0.137   2015
  Dihedral  :  4.836  27.147   1515
  Min Nonbonded Distance : 1.514

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.45 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.20 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.15 %
  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: -1.35 (0.23), residues: 1365
  helix:  1.29 (0.25), residues: 395
  sheet: -0.88 (0.26), residues: 375
  loop : -2.48 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D  99 
 TYR   0.010   0.001   TYR C 248 
 PHE   0.023   0.001   PHE B 119 
 TRP   0.010   0.001   TRP D 160 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (11640)
  covalent geometry    : angle       0.91777 (15865)
  hydrogen bonds       : bond        0.03089 (  495)
  hydrogen bonds       : angle       4.67499 ( 1620)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1830.03 seconds
wall clock time: 32 minutes 27.60 seconds (1947.60 seconds total)