Starting phenix.real_space_refine
on Sun May 18 19:18:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kef_37154/05_2025/8kef_37154_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kef_37154/05_2025/8kef_37154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kef_37154/05_2025/8kef_37154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kef_37154/05_2025/8kef_37154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kef_37154/05_2025/8kef_37154_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kef_37154/05_2025/8kef_37154_neut.cif"
  }
  resolution = 3.44
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.001
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      54      5.16       5
     C   11442      2.51       5
     N    2922      2.21       5
     O    3384      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 17802
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1041
          Classifications: {'peptide': 131}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 123}
    Chain: "a"
      Number of atoms: 1926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1926
          Classifications: {'peptide': 240}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 220}
  Restraints were copied for chains:
    C, B, E, D, F, f, c, b, e, d
  Time building chain proxies: 6.13, per 1000 atoms: 0.34
  Number of scatterers: 17802
  At special positions: 0
  Unit cell: (148.73, 150.87, 128.4, 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      54     16.00
     O    3384      8.00
     N    2922      7.00
     C   11442      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: 3.47
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4320

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 24 sheets defined
      20.8% alpha, 25.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 15
      removed outlier: 4.125A  pdb=" N   ASN A   8 " --> pdb=" O   SER A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 20
    Processing helix  chain 'A' and resid 81 through 87
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 4.126A  pdb=" N   ASN B   8 " --> pdb=" O   SER B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 20
    Processing helix  chain 'B' and resid 81 through 87
    Processing helix  chain 'C' and resid 4 through 15
      removed outlier: 4.125A  pdb=" N   ASN C   8 " --> pdb=" O   SER C   4 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 20
    Processing helix  chain 'C' and resid 81 through 87
    Processing helix  chain 'D' and resid 4 through 15
      removed outlier: 4.125A  pdb=" N   ASN D   8 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 20
    Processing helix  chain 'D' and resid 81 through 87
    Processing helix  chain 'E' and resid 4 through 15
      removed outlier: 4.126A  pdb=" N   ASN E   8 " --> pdb=" O   SER E   4 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 16 through 20
    Processing helix  chain 'E' and resid 81 through 87
    Processing helix  chain 'F' and resid 4 through 15
      removed outlier: 4.126A  pdb=" N   ASN F   8 " --> pdb=" O   SER F   4 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 20
    Processing helix  chain 'F' and resid 81 through 87
    Processing helix  chain 'a' and resid 2 through 16
    Processing helix  chain 'a' and resid 93 through 97
    Processing helix  chain 'a' and resid 98 through 116
    Processing helix  chain 'a' and resid 116 through 121
      removed outlier: 3.921A  pdb=" N   ASP a 121 " --> pdb=" O   TYR a 117 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 169 through 171
      No H-bonds generated for 'chain 'a' and resid 169 through 171'
    Processing helix  chain 'a' and resid 233 through 237
    Processing helix  chain 'b' and resid 2 through 16
    Processing helix  chain 'b' and resid 93 through 97
    Processing helix  chain 'b' and resid 98 through 116
    Processing helix  chain 'b' and resid 116 through 121
      removed outlier: 3.921A  pdb=" N   ASP b 121 " --> pdb=" O   TYR b 117 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 169 through 171
      No H-bonds generated for 'chain 'b' and resid 169 through 171'
    Processing helix  chain 'b' and resid 233 through 237
    Processing helix  chain 'c' and resid 2 through 16
    Processing helix  chain 'c' and resid 93 through 97
    Processing helix  chain 'c' and resid 98 through 116
    Processing helix  chain 'c' and resid 116 through 121
      removed outlier: 3.921A  pdb=" N   ASP c 121 " --> pdb=" O   TYR c 117 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 169 through 171
      No H-bonds generated for 'chain 'c' and resid 169 through 171'
    Processing helix  chain 'c' and resid 233 through 237
    Processing helix  chain 'd' and resid 2 through 16
    Processing helix  chain 'd' and resid 93 through 97
    Processing helix  chain 'd' and resid 98 through 116
    Processing helix  chain 'd' and resid 116 through 121
      removed outlier: 3.921A  pdb=" N   ASP d 121 " --> pdb=" O   TYR d 117 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 169 through 171
      No H-bonds generated for 'chain 'd' and resid 169 through 171'
    Processing helix  chain 'd' and resid 233 through 237
    Processing helix  chain 'e' and resid 2 through 16
    Processing helix  chain 'e' and resid 93 through 97
    Processing helix  chain 'e' and resid 98 through 116
    Processing helix  chain 'e' and resid 116 through 121
      removed outlier: 3.921A  pdb=" N   ASP e 121 " --> pdb=" O   TYR e 117 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 169 through 171
      No H-bonds generated for 'chain 'e' and resid 169 through 171'
    Processing helix  chain 'e' and resid 233 through 237
    Processing helix  chain 'f' and resid 2 through 16
    Processing helix  chain 'f' and resid 93 through 97
    Processing helix  chain 'f' and resid 98 through 116
    Processing helix  chain 'f' and resid 116 through 121
      removed outlier: 3.921A  pdb=" N   ASP f 121 " --> pdb=" O   TYR f 117 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 169 through 171
      No H-bonds generated for 'chain 'f' and resid 169 through 171'
    Processing helix  chain 'f' and resid 233 through 237
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39
      removed outlier: 5.368A  pdb=" N   CYS A 109 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   ARG A 125 " --> pdb=" O   CYS A 109 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU A 122 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   THR A  74 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU A 124 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   TYR A  72 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ASP A  70 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE A  66 " --> pdb=" O   MET A  53 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA A  68 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LYS A  51 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASP A  70 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A  49 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39
      removed outlier: 5.369A  pdb=" N   CYS B 109 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ARG B 125 " --> pdb=" O   CYS B 109 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU B 122 " --> pdb=" O   THR B  74 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   THR B  74 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU B 124 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   TYR B  72 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LYS B 126 " --> pdb=" O   ASP B  70 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ASP B  70 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE B  66 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   MET B  53 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA B  68 " --> pdb=" O   LYS B  51 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LYS B  51 " --> pdb=" O   ALA B  68 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ASP B  70 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B  49 " --> pdb=" O   ASP B  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39
      removed outlier: 5.369A  pdb=" N   CYS C 109 " --> pdb=" O   ARG C 125 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ARG C 125 " --> pdb=" O   CYS C 109 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU C 122 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   THR C  74 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU C 124 " --> pdb=" O   TYR C  72 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   TYR C  72 " --> pdb=" O   LEU C 124 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LYS C 126 " --> pdb=" O   ASP C  70 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ASP C  70 " --> pdb=" O   LYS C 126 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE C  66 " --> pdb=" O   MET C  53 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   MET C  53 " --> pdb=" O   ILE C  66 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA C  68 " --> pdb=" O   LYS C  51 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LYS C  51 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASP C  70 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL C  49 " --> pdb=" O   ASP C  70 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 38 through 39
      removed outlier: 5.368A  pdb=" N   CYS D 109 " --> pdb=" O   ARG D 125 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   ARG D 125 " --> pdb=" O   CYS D 109 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU D 122 " --> pdb=" O   THR D  74 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   THR D  74 " --> pdb=" O   LEU D 122 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU D 124 " --> pdb=" O   TYR D  72 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   TYR D  72 " --> pdb=" O   LEU D 124 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LYS D 126 " --> pdb=" O   ASP D  70 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ASP D  70 " --> pdb=" O   LYS D 126 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ILE D  66 " --> pdb=" O   MET D  53 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   MET D  53 " --> pdb=" O   ILE D  66 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA D  68 " --> pdb=" O   LYS D  51 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LYS D  51 " --> pdb=" O   ALA D  68 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASP D  70 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL D  49 " --> pdb=" O   ASP D  70 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39
      removed outlier: 5.369A  pdb=" N   CYS E 109 " --> pdb=" O   ARG E 125 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ARG E 125 " --> pdb=" O   CYS E 109 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU E 122 " --> pdb=" O   THR E  74 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   THR E  74 " --> pdb=" O   LEU E 122 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU E 124 " --> pdb=" O   TYR E  72 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   TYR E  72 " --> pdb=" O   LEU E 124 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LYS E 126 " --> pdb=" O   ASP E  70 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ASP E  70 " --> pdb=" O   LYS E 126 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE E  66 " --> pdb=" O   MET E  53 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   MET E  53 " --> pdb=" O   ILE E  66 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA E  68 " --> pdb=" O   LYS E  51 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LYS E  51 " --> pdb=" O   ALA E  68 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ASP E  70 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL E  49 " --> pdb=" O   ASP E  70 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 38 through 39
      removed outlier: 5.370A  pdb=" N   CYS F 109 " --> pdb=" O   ARG F 125 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ARG F 125 " --> pdb=" O   CYS F 109 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU F 122 " --> pdb=" O   THR F  74 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   THR F  74 " --> pdb=" O   LEU F 122 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU F 124 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   TYR F  72 " --> pdb=" O   LEU F 124 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LYS F 126 " --> pdb=" O   ASP F  70 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ASP F  70 " --> pdb=" O   LYS F 126 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE F  66 " --> pdb=" O   MET F  53 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   MET F  53 " --> pdb=" O   ILE F  66 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA F  68 " --> pdb=" O   LYS F  51 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   LYS F  51 " --> pdb=" O   ALA F  68 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASP F  70 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL F  49 " --> pdb=" O   ASP F  70 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 36
    Processing sheet with id=AA8, first strand: chain 'a' and resid 44 through 48
  WARNING: can't find start of bonding for strands!
    previous: chain 'a' and resid 44 through 48
    current: chain 'a' and resid 71 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'a' and resid 71 through 86
    current: chain 'a' and resid 150 through 167
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'a' and resid 205 through 211
      removed outlier: 3.585A  pdb=" N   LEU a 208 " --> pdb=" O   GLU a 228 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU a 228 " --> pdb=" O   LEU a 208 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   LYS a 210 " --> pdb=" O   LEU a 226 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU a 226 " --> pdb=" O   LYS a 210 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'b' and resid 34 through 36
    Processing sheet with id=AB2, first strand: chain 'b' and resid 44 through 48
  WARNING: can't find start of bonding for strands!
    previous: chain 'b' and resid 44 through 48
    current: chain 'b' and resid 71 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'b' and resid 71 through 86
    current: chain 'b' and resid 150 through 167
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'b' and resid 205 through 211
      removed outlier: 3.586A  pdb=" N   LEU b 208 " --> pdb=" O   GLU b 228 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU b 228 " --> pdb=" O   LEU b 208 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   LYS b 210 " --> pdb=" O   LEU b 226 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU b 226 " --> pdb=" O   LYS b 210 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'c' and resid 34 through 36
    Processing sheet with id=AB5, first strand: chain 'c' and resid 44 through 48
  WARNING: can't find start of bonding for strands!
    previous: chain 'c' and resid 44 through 48
    current: chain 'c' and resid 71 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'c' and resid 71 through 86
    current: chain 'c' and resid 150 through 167
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'c' and resid 205 through 211
      removed outlier: 3.586A  pdb=" N   LEU c 208 " --> pdb=" O   GLU c 228 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU c 228 " --> pdb=" O   LEU c 208 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   LYS c 210 " --> pdb=" O   LEU c 226 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU c 226 " --> pdb=" O   LYS c 210 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'd' and resid 34 through 36
    Processing sheet with id=AB8, first strand: chain 'd' and resid 44 through 48
  WARNING: can't find start of bonding for strands!
    previous: chain 'd' and resid 44 through 48
    current: chain 'd' and resid 71 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'd' and resid 71 through 86
    current: chain 'd' and resid 150 through 167
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'd' and resid 205 through 211
      removed outlier: 3.585A  pdb=" N   LEU d 208 " --> pdb=" O   GLU d 228 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU d 228 " --> pdb=" O   LEU d 208 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   LYS d 210 " --> pdb=" O   LEU d 226 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU d 226 " --> pdb=" O   LYS d 210 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'e' and resid 34 through 36
    Processing sheet with id=AC2, first strand: chain 'e' and resid 44 through 48
  WARNING: can't find start of bonding for strands!
    previous: chain 'e' and resid 44 through 48
    current: chain 'e' and resid 71 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'e' and resid 71 through 86
    current: chain 'e' and resid 150 through 167
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'e' and resid 205 through 211
      removed outlier: 3.586A  pdb=" N   LEU e 208 " --> pdb=" O   GLU e 228 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU e 228 " --> pdb=" O   LEU e 208 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   LYS e 210 " --> pdb=" O   LEU e 226 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU e 226 " --> pdb=" O   LYS e 210 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'f' and resid 34 through 36
    Processing sheet with id=AC5, first strand: chain 'f' and resid 44 through 48
  WARNING: can't find start of bonding for strands!
    previous: chain 'f' and resid 44 through 48
    current: chain 'f' and resid 71 through 86
  WARNING: can't find start of bonding for strands!
    previous: chain 'f' and resid 71 through 86
    current: chain 'f' and resid 150 through 167
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'f' and resid 205 through 211
      removed outlier: 3.586A  pdb=" N   LEU f 208 " --> pdb=" O   GLU f 228 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU f 228 " --> pdb=" O   LEU f 208 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   LYS f 210 " --> pdb=" O   LEU f 226 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU f 226 " --> pdb=" O   LYS f 210 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    918 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: 4.84

  Time building geometry restraints manager: 4.08 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 3018
        1.30 -     1.43: 4391
        1.43 -     1.57: 10625
        1.57 -     1.70: 56
        1.70 -     1.83: 84
  Bond restraints: 18174
  Sorted by residual:
  bond pdb=" C   ARG E  17 "
       pdb=" O   ARG E  17 "
    ideal  model  delta    sigma   weight residual
    1.237  1.172  0.065 1.17e-02 7.31e+03 3.06e+01
  bond pdb=" C   ARG A  17 "
       pdb=" O   ARG A  17 "
    ideal  model  delta    sigma   weight residual
    1.237  1.172  0.064 1.17e-02 7.31e+03 3.02e+01
  bond pdb=" C   ARG D  17 "
       pdb=" O   ARG D  17 "
    ideal  model  delta    sigma   weight residual
    1.237  1.173  0.064 1.17e-02 7.31e+03 3.01e+01
  bond pdb=" C   ARG F  17 "
       pdb=" O   ARG F  17 "
    ideal  model  delta    sigma   weight residual
    1.237  1.173  0.064 1.17e-02 7.31e+03 3.01e+01
  bond pdb=" C   ARG C  17 "
       pdb=" O   ARG C  17 "
    ideal  model  delta    sigma   weight residual
    1.237  1.173  0.064 1.17e-02 7.31e+03 3.01e+01
  ... (remaining 18169 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 18088
        1.93 -     3.87: 5430
        3.87 -     5.80: 1082
        5.80 -     7.74: 138
        7.74 -     9.67: 36
  Bond angle restraints: 24774
  Sorted by residual:
  angle pdb=" CA  ASP A  22 "
        pdb=" CB  ASP A  22 "
        pdb=" CG  ASP A  22 "
      ideal   model   delta    sigma   weight residual
     112.60  120.47   -7.87 1.00e+00 1.00e+00 6.20e+01
  angle pdb=" CA  ASP D  22 "
        pdb=" CB  ASP D  22 "
        pdb=" CG  ASP D  22 "
      ideal   model   delta    sigma   weight residual
     112.60  120.47   -7.87 1.00e+00 1.00e+00 6.20e+01
  angle pdb=" CA  ASP F  22 "
        pdb=" CB  ASP F  22 "
        pdb=" CG  ASP F  22 "
      ideal   model   delta    sigma   weight residual
     112.60  120.42   -7.82 1.00e+00 1.00e+00 6.12e+01
  angle pdb=" CA  ASP C  22 "
        pdb=" CB  ASP C  22 "
        pdb=" CG  ASP C  22 "
      ideal   model   delta    sigma   weight residual
     112.60  120.42   -7.82 1.00e+00 1.00e+00 6.12e+01
  angle pdb=" CA  ASP B  22 "
        pdb=" CB  ASP B  22 "
        pdb=" CG  ASP B  22 "
      ideal   model   delta    sigma   weight residual
     112.60  120.41   -7.81 1.00e+00 1.00e+00 6.11e+01
  ... (remaining 24769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.89: 9972
       16.89 -    33.77: 944
       33.77 -    50.66: 208
       50.66 -    67.54: 54
       67.54 -    84.43: 30
  Dihedral angle restraints: 11208
    sinusoidal: 4602
      harmonic: 6606
  Sorted by residual:
  dihedral pdb=" N   TYR C   3 "
           pdb=" C   TYR C   3 "
           pdb=" CA  TYR C   3 "
           pdb=" CB  TYR C   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.15  -13.35     0      2.50e+00 1.60e-01 2.85e+01
  dihedral pdb=" N   TYR F   3 "
           pdb=" C   TYR F   3 "
           pdb=" CA  TYR F   3 "
           pdb=" CB  TYR F   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.15  -13.35     0      2.50e+00 1.60e-01 2.85e+01
  dihedral pdb=" N   TYR A   3 "
           pdb=" C   TYR A   3 "
           pdb=" CA  TYR A   3 "
           pdb=" CB  TYR A   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.13  -13.33     0      2.50e+00 1.60e-01 2.84e+01
  ... (remaining 11205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 2068
       0.107 -    0.213: 687
       0.213 -    0.319: 137
       0.319 -    0.426: 12
       0.426 -    0.532: 18
  Chirality restraints: 2922
  Sorted by residual:
  chirality pdb=" CA  THR c 183 "
            pdb=" N   THR c 183 "
            pdb=" C   THR c 183 "
            pdb=" CB  THR c 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.99    0.53 2.00e-01 2.50e+01 7.09e+00
  chirality pdb=" CA  THR f 183 "
            pdb=" N   THR f 183 "
            pdb=" C   THR f 183 "
            pdb=" CB  THR f 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.99    0.53 2.00e-01 2.50e+01 7.09e+00
  chirality pdb=" CA  THR d 183 "
            pdb=" N   THR d 183 "
            pdb=" C   THR d 183 "
            pdb=" CB  THR d 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.00    0.53 2.00e-01 2.50e+01 7.05e+00
  ... (remaining 2919 not shown)

  Planarity restraints: 3174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP a 184 "    0.088 2.00e-02 2.50e+03   4.31e-02 4.65e+01
        pdb=" CG  TRP a 184 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP a 184 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TRP a 184 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP a 184 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP a 184 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP a 184 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ2 TRP a 184 "    0.051 2.00e-02 2.50e+03
        pdb=" CZ3 TRP a 184 "   -0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP a 184 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP e 184 "   -0.088 2.00e-02 2.50e+03   4.31e-02 4.65e+01
        pdb=" CG  TRP e 184 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP e 184 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 TRP e 184 "    0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP e 184 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP e 184 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP e 184 "    0.050 2.00e-02 2.50e+03
        pdb=" CZ2 TRP e 184 "   -0.051 2.00e-02 2.50e+03
        pdb=" CZ3 TRP e 184 "    0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP e 184 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP d 184 "   -0.088 2.00e-02 2.50e+03   4.31e-02 4.64e+01
        pdb=" CG  TRP d 184 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP d 184 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 TRP d 184 "    0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP d 184 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP d 184 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP d 184 "    0.049 2.00e-02 2.50e+03
        pdb=" CZ2 TRP d 184 "   -0.051 2.00e-02 2.50e+03
        pdb=" CZ3 TRP d 184 "    0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP d 184 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 3171 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 96
        2.57 -     3.15: 13569
        3.15 -     3.74: 27435
        3.74 -     4.32: 38080
        4.32 -     4.90: 61603
  Nonbonded interactions: 140783
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN d  16 "
            pdb=" N   ILE e 193 "
     model   vdw
     1.989 3.120
  nonbonded pdb=" N   ILE a 193 "
            pdb=" OD1 ASN f  16 "
     model   vdw
     1.990 3.120
  nonbonded pdb=" OD1 ASN c  16 "
            pdb=" N   ILE d 193 "
     model   vdw
     1.990 3.120
  nonbonded pdb=" OD1 ASN b  16 "
            pdb=" N   ILE c 193 "
     model   vdw
     1.990 3.120
  nonbonded pdb=" OD1 ASN e  16 "
            pdb=" N   ILE f 193 "
     model   vdw
     1.990 3.120
  ... (remaining 140778 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'a'
  selection = chain 'f'
  selection = chain 'c'
  selection = chain 'b'
  selection = chain 'e'
  selection = chain 'd'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.680
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     32.550
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
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      :  0.015   0.065  18174  Z= 0.896
  Angle     :  1.897   9.669  24774  Z= 1.299
  Chirality :  0.113   0.532   2922
  Planarity :  0.013   0.080   3174
  Dihedral  : 14.960  84.429   6888
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.80 %
    Favored  : 82.76 %
  Cbeta Deviations :  1.39 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.17), residues: 2202
  helix:  1.60 (0.26), residues: 264
  sheet:  0.04 (0.21), residues: 564
  loop : -0.91 (0.16), residues: 1374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.088   0.022   TRP a 184 
 HIS   0.004   0.002   HIS B 110 
 PHE   0.038   0.011   PHE a  78 
 TYR   0.080   0.023   TYR e  94 
 ARG   0.030   0.007   ARG D 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17809 (  396)
  hydrogen bonds       : angle       6.99567 (  918)
  covalent geometry    : bond        0.01536 (18174)
  covalent geometry    : angle       1.89670 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 309
  time to evaluate  : 2.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: b  118 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6826 (pm20)
REVERT: c  118 GLN cc_start: 0.7361 (tp-100) cc_final: 0.6866 (pm20)
REVERT: e  118 GLN cc_start: 0.7223 (tp-100) cc_final: 0.6828 (pm20)
REVERT: f  118 GLN cc_start: 0.7353 (tp-100) cc_final: 0.6868 (pm20)
  outliers start: 30
  outliers final: 6
  residues processed: 329
  average time/residue: 0.2887
  time to fit residues: 143.4755
Evaluate side-chains
  259 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 253
  time to evaluate  : 1.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain c residue   45 VAL
Chi-restraints excluded: chain f residue   45 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 187 optimal weight:    0.9980
   chunk 168 optimal weight:    8.9990
   chunk 93 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 113 optimal weight:    8.9990
   chunk 89 optimal weight:    3.9990
   chunk 174 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 129 optimal weight:    5.9990
   chunk 201 optimal weight:    9.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 180 GLN
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 180 GLN
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c 180 GLN
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 180 GLN
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
e 180 GLN
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f 180 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.073024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.064458 restraints weight = 63037.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 3.41
r_work: 0.3033 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  18174  Z= 0.180
  Angle     :  0.616   6.765  24774  Z= 0.319
  Chirality :  0.048   0.170   2922
  Planarity :  0.006   0.058   3174
  Dihedral  :  4.925  20.058   2394
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.92 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.18), residues: 2202
  helix:  1.03 (0.31), residues: 258
  sheet: -0.07 (0.22), residues: 516
  loop : -0.31 (0.17), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP a  84 
 HIS   0.004   0.001   HIS a  14 
 PHE   0.010   0.001   PHE e  78 
 TYR   0.013   0.001   TYR A 120 
 ARG   0.005   0.001   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04712 (  396)
  hydrogen bonds       : angle       6.27444 (  918)
  covalent geometry    : bond        0.00423 (18174)
  covalent geometry    : angle       0.61588 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 218
  time to evaluate  : 1.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.8323 (tpt) cc_final: 0.7869 (tpt)
REVERT: B   72 TYR cc_start: 0.8966 (t80) cc_final: 0.8745 (t80)
REVERT: C   53 MET cc_start: 0.8398 (tpt) cc_final: 0.7835 (tpt)
REVERT: E   53 MET cc_start: 0.8355 (tpt) cc_final: 0.7905 (tpt)
REVERT: E   72 TYR cc_start: 0.8979 (t80) cc_final: 0.8764 (t80)
REVERT: F   53 MET cc_start: 0.8389 (tpt) cc_final: 0.7825 (tpt)
REVERT: f   16 ASN cc_start: 0.7657 (t0) cc_final: 0.7396 (t0)
  outliers start: 32
  outliers final: 23
  residues processed: 244
  average time/residue: 0.2792
  time to fit residues: 103.7993
Evaluate side-chains
  229 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 1.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain a residue  237 GLU
Chi-restraints excluded: chain c residue  193 ILE
Chi-restraints excluded: chain d residue  193 ILE
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain d residue  237 GLU
Chi-restraints excluded: chain f residue  193 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 180 optimal weight:    0.0000
   chunk 200 optimal weight:    8.9990
   chunk 115 optimal weight:    6.9990
   chunk 179 optimal weight:    2.9990
   chunk 166 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 56 optimal weight:   40.0000
   chunk 69 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 216 optimal weight:    5.9990
   chunk 204 optimal weight:    3.9990
   overall best weight:    2.3790

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.073582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.064946 restraints weight = 62275.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 3.38
r_work: 0.3050 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  18174  Z= 0.119
  Angle     :  0.569   7.460  24774  Z= 0.288
  Chirality :  0.048   0.174   2922
  Planarity :  0.005   0.049   3174
  Dihedral  :  4.581  19.861   2392
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 18.87 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.18), residues: 2202
  helix:  1.10 (0.31), residues: 258
  sheet:  0.28 (0.24), residues: 444
  loop : -0.22 (0.17), residues: 1500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP d  84 
 HIS   0.003   0.001   HIS b  95 
 PHE   0.012   0.001   PHE c  78 
 TYR   0.012   0.001   TYR A 120 
 ARG   0.003   0.000   ARG F  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  396)
  hydrogen bonds       : angle       5.76738 (  918)
  covalent geometry    : bond        0.00279 (18174)
  covalent geometry    : angle       0.56912 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 235
  time to evaluate  : 2.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8018 (tpt) cc_final: 0.7724 (tpt)
REVERT: A   92 ASP cc_start: 0.8584 (m-30) cc_final: 0.8351 (m-30)
REVERT: B   53 MET cc_start: 0.8287 (tpt) cc_final: 0.7806 (tpt)
REVERT: B  121 ASP cc_start: 0.8195 (t0) cc_final: 0.7984 (t0)
REVERT: C   18 GLU cc_start: 0.7820 (mp0) cc_final: 0.7248 (mp0)
REVERT: C   53 MET cc_start: 0.8279 (tpt) cc_final: 0.7756 (tpt)
REVERT: D   53 MET cc_start: 0.8030 (tpt) cc_final: 0.7740 (tpt)
REVERT: D   92 ASP cc_start: 0.8582 (m-30) cc_final: 0.8350 (m-30)
REVERT: E   53 MET cc_start: 0.8320 (tpt) cc_final: 0.7837 (tpt)
REVERT: E  121 ASP cc_start: 0.8201 (t0) cc_final: 0.7991 (t0)
REVERT: F   18 GLU cc_start: 0.7822 (mp0) cc_final: 0.7253 (mp0)
REVERT: F   53 MET cc_start: 0.8286 (tpt) cc_final: 0.7762 (tpt)
REVERT: b  118 GLN cc_start: 0.9005 (tp-100) cc_final: 0.7018 (pm20)
REVERT: c   62 MET cc_start: 0.8336 (mtp) cc_final: 0.6843 (tpt)
REVERT: e  118 GLN cc_start: 0.8999 (tp-100) cc_final: 0.7011 (pm20)
REVERT: f   62 MET cc_start: 0.8267 (mtp) cc_final: 0.6730 (tpt)
  outliers start: 73
  outliers final: 43
  residues processed: 286
  average time/residue: 0.2959
  time to fit residues: 128.1176
Evaluate side-chains
  258 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 215
  time to evaluate  : 1.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   75 ASP
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain E residue  123 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain a residue  237 GLU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain c residue  193 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain d residue  237 GLU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Chi-restraints excluded: chain f residue  193 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 194 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 2 optimal weight:   20.0000
   chunk 100 optimal weight:    0.0570
   chunk 9 optimal weight:    1.9990
   chunk 215 optimal weight:    2.9990
   chunk 103 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    2.2106

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

Flipped N/Q/H residues before XYZ refinement:
B   8 ASN
B  79 ASN
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.073664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.065048 restraints weight = 62157.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 3.35
r_work: 0.3056 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  18174  Z= 0.121
  Angle     :  0.571   7.394  24774  Z= 0.287
  Chirality :  0.049   0.184   2922
  Planarity :  0.005   0.045   3174
  Dihedral  :  4.476  25.614   2392
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.83 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.18), residues: 2202
  helix:  0.95 (0.31), residues: 258
  sheet:  0.21 (0.24), residues: 444
  loop : -0.17 (0.17), residues: 1500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  90 
 HIS   0.003   0.001   HIS b  95 
 PHE   0.008   0.001   PHE a  78 
 TYR   0.012   0.001   TYR E 120 
 ARG   0.007   0.000   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03744 (  396)
  hydrogen bonds       : angle       5.70360 (  918)
  covalent geometry    : bond        0.00287 (18174)
  covalent geometry    : angle       0.57062 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 228
  time to evaluate  : 2.033 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8081 (tpt) cc_final: 0.7691 (tpt)
REVERT: A   92 ASP cc_start: 0.8578 (m-30) cc_final: 0.8320 (m-30)
REVERT: B   53 MET cc_start: 0.8210 (tpt) cc_final: 0.7703 (tpt)
REVERT: C   53 MET cc_start: 0.8156 (tpt) cc_final: 0.7622 (tpt)
REVERT: D   53 MET cc_start: 0.8093 (tpt) cc_final: 0.7705 (tpt)
REVERT: D   92 ASP cc_start: 0.8581 (m-30) cc_final: 0.8323 (m-30)
REVERT: E   53 MET cc_start: 0.8235 (tpt) cc_final: 0.7728 (tpt)
REVERT: F   53 MET cc_start: 0.8152 (tpt) cc_final: 0.7619 (tpt)
REVERT: a    1 MET cc_start: 0.6440 (mpp) cc_final: 0.5973 (mtp)
REVERT: a  118 GLN cc_start: 0.4527 (pm20) cc_final: 0.4325 (pm20)
REVERT: a  169 ASP cc_start: 0.8657 (m-30) cc_final: 0.8453 (m-30)
REVERT: b   16 ASN cc_start: 0.7681 (t0) cc_final: 0.7391 (t0)
REVERT: b   62 MET cc_start: 0.8180 (ttm) cc_final: 0.6618 (tpt)
REVERT: b  118 GLN cc_start: 0.9000 (tp-100) cc_final: 0.6990 (pm20)
REVERT: c   62 MET cc_start: 0.8421 (mtp) cc_final: 0.6792 (tpt)
REVERT: d    1 MET cc_start: 0.6441 (mpp) cc_final: 0.5976 (mtp)
REVERT: d  118 GLN cc_start: 0.4526 (pm20) cc_final: 0.4318 (pm20)
REVERT: d  169 ASP cc_start: 0.8643 (m-30) cc_final: 0.8439 (m-30)
REVERT: e   16 ASN cc_start: 0.7695 (t0) cc_final: 0.7407 (t0)
REVERT: e   62 MET cc_start: 0.8174 (ttm) cc_final: 0.6615 (tpt)
REVERT: e  118 GLN cc_start: 0.8996 (tp-100) cc_final: 0.6985 (pm20)
REVERT: f   62 MET cc_start: 0.8350 (mtp) cc_final: 0.6694 (tpt)
  outliers start: 57
  outliers final: 45
  residues processed: 270
  average time/residue: 0.2881
  time to fit residues: 117.3048
Evaluate side-chains
  263 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 218
  time to evaluate  : 1.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   75 ASP
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain E residue  123 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  193 ILE
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain a residue  237 GLU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain c residue  193 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain d residue  237 GLU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Chi-restraints excluded: chain f residue  193 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 181 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 129 optimal weight:   30.0000
   chunk 50 optimal weight:   30.0000
   chunk 200 optimal weight:   20.0000
   chunk 125 optimal weight:    7.9990
   chunk 151 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 171 optimal weight:    6.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.071538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.062870 restraints weight = 63541.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 3.38
r_work: 0.2993 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  18174  Z= 0.187
  Angle     :  0.601   7.894  24774  Z= 0.299
  Chirality :  0.049   0.193   2922
  Planarity :  0.004   0.045   3174
  Dihedral  :  4.566  25.579   2392
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.59 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.18), residues: 2202
  helix:  0.81 (0.31), residues: 258
  sheet: -0.43 (0.21), residues: 516
  loop : -0.13 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  90 
 HIS   0.004   0.002   HIS f  14 
 PHE   0.008   0.001   PHE f 171 
 TYR   0.009   0.001   TYR a 117 
 ARG   0.003   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  396)
  hydrogen bonds       : angle       5.49489 (  918)
  covalent geometry    : bond        0.00446 (18174)
  covalent geometry    : angle       0.60136 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 221
  time to evaluate  : 2.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7823 (mp0) cc_final: 0.7248 (mp0)
REVERT: A   92 ASP cc_start: 0.8575 (m-30) cc_final: 0.8316 (m-30)
REVERT: B   18 GLU cc_start: 0.7718 (mp0) cc_final: 0.7112 (mp0)
REVERT: B   53 MET cc_start: 0.8322 (tpt) cc_final: 0.7891 (tpt)
REVERT: C   18 GLU cc_start: 0.7773 (mp0) cc_final: 0.7148 (mp0)
REVERT: C   53 MET cc_start: 0.8308 (tpt) cc_final: 0.7819 (tpt)
REVERT: D   18 GLU cc_start: 0.7859 (mp0) cc_final: 0.7273 (mp0)
REVERT: D   92 ASP cc_start: 0.8573 (m-30) cc_final: 0.8315 (m-30)
REVERT: E   18 GLU cc_start: 0.7675 (mp0) cc_final: 0.7068 (mp0)
REVERT: E   53 MET cc_start: 0.8324 (tpt) cc_final: 0.7896 (tpt)
REVERT: F   18 GLU cc_start: 0.7764 (mp0) cc_final: 0.7139 (mp0)
REVERT: F   53 MET cc_start: 0.8351 (tpt) cc_final: 0.7876 (tpt)
REVERT: b  117 TYR cc_start: 0.8633 (m-80) cc_final: 0.8392 (m-80)
REVERT: b  118 GLN cc_start: 0.9133 (tp-100) cc_final: 0.7277 (pm20)
REVERT: e  117 TYR cc_start: 0.8642 (m-80) cc_final: 0.8404 (m-80)
REVERT: e  118 GLN cc_start: 0.9137 (tp-100) cc_final: 0.7281 (pm20)
  outliers start: 65
  outliers final: 42
  residues processed: 268
  average time/residue: 0.2903
  time to fit residues: 117.3226
Evaluate side-chains
  251 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 209
  time to evaluate  : 2.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   75 ASP
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  113 ASN
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   75 ASP
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain c residue  193 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Chi-restraints excluded: chain f residue  193 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 127 optimal weight:    0.9990
   chunk 179 optimal weight:    0.9990
   chunk 136 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 137 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 113 ASN
E   8 ASN
E  79 ASN
E 113 ASN
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.073076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.064397 restraints weight = 62143.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 3.41
r_work: 0.3032 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  18174  Z= 0.110
  Angle     :  0.561   7.719  24774  Z= 0.280
  Chirality :  0.048   0.184   2922
  Planarity :  0.004   0.041   3174
  Dihedral  :  4.413  25.144   2392
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.70 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.19), residues: 2202
  helix:  0.92 (0.31), residues: 258
  sheet: -0.44 (0.21), residues: 516
  loop : -0.13 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a  84 
 HIS   0.002   0.001   HIS d  95 
 PHE   0.009   0.001   PHE f  78 
 TYR   0.010   0.001   TYR D 120 
 ARG   0.002   0.000   ARG F  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  396)
  hydrogen bonds       : angle       5.35871 (  918)
  covalent geometry    : bond        0.00262 (18174)
  covalent geometry    : angle       0.56066 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 236
  time to evaluate  : 2.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8140 (tpt) cc_final: 0.7820 (tpt)
REVERT: A   92 ASP cc_start: 0.8510 (m-30) cc_final: 0.8245 (m-30)
REVERT: B   53 MET cc_start: 0.8218 (tpt) cc_final: 0.7796 (tpt)
REVERT: C   53 MET cc_start: 0.8167 (tpt) cc_final: 0.7724 (tpt)
REVERT: D   53 MET cc_start: 0.8167 (tpt) cc_final: 0.7848 (tpt)
REVERT: D   92 ASP cc_start: 0.8513 (m-30) cc_final: 0.8253 (m-30)
REVERT: E   53 MET cc_start: 0.8223 (tpt) cc_final: 0.7802 (tpt)
REVERT: F   53 MET cc_start: 0.8153 (tpt) cc_final: 0.7715 (tpt)
REVERT: a    1 MET cc_start: 0.6347 (mpp) cc_final: 0.5857 (mtp)
REVERT: b   62 MET cc_start: 0.8265 (ttm) cc_final: 0.6729 (tpt)
REVERT: b  117 TYR cc_start: 0.8529 (m-80) cc_final: 0.8324 (m-80)
REVERT: b  118 GLN cc_start: 0.9050 (tp-100) cc_final: 0.7172 (pm20)
REVERT: b  163 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8554 (mt-10)
REVERT: c   62 MET cc_start: 0.8239 (mtp) cc_final: 0.6698 (tpt)
REVERT: c  118 GLN cc_start: 0.9051 (tp-100) cc_final: 0.7167 (pm20)
REVERT: d    1 MET cc_start: 0.6320 (mpp) cc_final: 0.5835 (mtp)
REVERT: e   62 MET cc_start: 0.8270 (ttm) cc_final: 0.6733 (tpt)
REVERT: e  118 GLN cc_start: 0.9055 (tp-100) cc_final: 0.7177 (pm20)
REVERT: e  163 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8543 (mt-10)
REVERT: f   62 MET cc_start: 0.8092 (mtp) cc_final: 0.6651 (tpt)
REVERT: f  118 GLN cc_start: 0.9053 (tp-100) cc_final: 0.7102 (pm20)
  outliers start: 63
  outliers final: 44
  residues processed: 291
  average time/residue: 0.3021
  time to fit residues: 131.3992
Evaluate side-chains
  265 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 219
  time to evaluate  : 1.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  113 ASN
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  123 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain a residue  237 GLU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain b residue  163 GLU
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain c residue  193 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain d residue  237 GLU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain e residue  163 GLU
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Chi-restraints excluded: chain f residue  193 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 193 optimal weight:   30.0000
   chunk 27 optimal weight:    0.0070
   chunk 209 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 154 optimal weight:    0.9990
   chunk 30 optimal weight:   50.0000
   chunk 159 optimal weight:    2.9990
   chunk 141 optimal weight:    5.9990
   chunk 213 optimal weight:   20.0000
   chunk 133 optimal weight:    9.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    3.0006

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

Flipped N/Q/H residues before XYZ refinement:
a  16 ASN
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  16 ASN
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.072566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.064010 restraints weight = 62561.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 3.36
r_work: 0.3023 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18174  Z= 0.134
  Angle     :  0.572   7.690  24774  Z= 0.284
  Chirality :  0.049   0.182   2922
  Planarity :  0.004   0.041   3174
  Dihedral  :  4.361  24.865   2392
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.22 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.19), residues: 2202
  helix:  1.07 (0.31), residues: 258
  sheet: -0.41 (0.21), residues: 516
  loop : -0.11 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  90 
 HIS   0.003   0.001   HIS d  14 
 PHE   0.007   0.001   PHE a 171 
 TYR   0.022   0.001   TYR B 120 
 ARG   0.003   0.000   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  396)
  hydrogen bonds       : angle       5.29840 (  918)
  covalent geometry    : bond        0.00325 (18174)
  covalent geometry    : angle       0.57197 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 231
  time to evaluate  : 1.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7738 (mp0) cc_final: 0.7136 (mp0)
REVERT: A   92 ASP cc_start: 0.8544 (m-30) cc_final: 0.8304 (m-30)
REVERT: B   18 GLU cc_start: 0.7731 (mp0) cc_final: 0.7080 (mp0)
REVERT: B   32 TYR cc_start: 0.8110 (t80) cc_final: 0.7871 (t80)
REVERT: B   37 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8748 (mt)
REVERT: B   51 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9215 (mtmt)
REVERT: B   53 MET cc_start: 0.8262 (tpt) cc_final: 0.7860 (tpt)
REVERT: B  118 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9013 (pt)
REVERT: C   18 GLU cc_start: 0.7752 (mp0) cc_final: 0.7116 (mp0)
REVERT: C   53 MET cc_start: 0.8205 (tpt) cc_final: 0.7869 (tpt)
REVERT: D   18 GLU cc_start: 0.7736 (mp0) cc_final: 0.7128 (mp0)
REVERT: D   92 ASP cc_start: 0.8545 (m-30) cc_final: 0.8306 (m-30)
REVERT: E   18 GLU cc_start: 0.7751 (mp0) cc_final: 0.7105 (mp0)
REVERT: E   32 TYR cc_start: 0.8126 (t80) cc_final: 0.7886 (t80)
REVERT: E   37 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8753 (mt)
REVERT: E   51 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9219 (mtmt)
REVERT: E   53 MET cc_start: 0.8270 (tpt) cc_final: 0.7865 (tpt)
REVERT: E  118 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9030 (pt)
REVERT: F   18 GLU cc_start: 0.7746 (mp0) cc_final: 0.7109 (mp0)
REVERT: F   53 MET cc_start: 0.8183 (tpt) cc_final: 0.7851 (tpt)
REVERT: b   62 MET cc_start: 0.8396 (ttm) cc_final: 0.6784 (tpt)
REVERT: b  118 GLN cc_start: 0.9066 (tp-100) cc_final: 0.7263 (pm20)
REVERT: b  163 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8507 (mt-10)
REVERT: c   62 MET cc_start: 0.7872 (mtp) cc_final: 0.6929 (tpt)
REVERT: c  118 GLN cc_start: 0.9076 (tp-100) cc_final: 0.7086 (pm20)
REVERT: e   62 MET cc_start: 0.8392 (ttm) cc_final: 0.6782 (tpt)
REVERT: e  118 GLN cc_start: 0.9066 (tp-100) cc_final: 0.7287 (pm20)
REVERT: e  163 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8484 (mt-10)
REVERT: f   62 MET cc_start: 0.7881 (mtp) cc_final: 0.6801 (tpt)
REVERT: f  118 GLN cc_start: 0.9076 (tp-100) cc_final: 0.7088 (pm20)
  outliers start: 78
  outliers final: 43
  residues processed: 297
  average time/residue: 0.2918
  time to fit residues: 130.1537
Evaluate side-chains
  272 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 221
  time to evaluate  : 1.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   51 LYS
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  113 ASN
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   51 LYS
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain a residue  237 GLU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain b residue  163 GLU
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain e residue  163 GLU
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 157 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 41 optimal weight:   20.0000
   chunk 153 optimal weight:   20.0000
   chunk 154 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   chunk 207 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 199 optimal weight:    6.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** a  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.071017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.062398 restraints weight = 62675.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 3.33
r_work: 0.2990 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  18174  Z= 0.186
  Angle     :  0.604   8.313  24774  Z= 0.300
  Chirality :  0.049   0.191   2922
  Planarity :  0.004   0.041   3174
  Dihedral  :  4.525  25.753   2392
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.22 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.19), residues: 2202
  helix:  0.85 (0.31), residues: 258
  sheet: -0.50 (0.21), residues: 516
  loop : -0.13 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  90 
 HIS   0.005   0.001   HIS d  14 
 PHE   0.010   0.001   PHE a  78 
 TYR   0.025   0.001   TYR B 120 
 ARG   0.004   0.000   ARG E  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  396)
  hydrogen bonds       : angle       5.33867 (  918)
  covalent geometry    : bond        0.00445 (18174)
  covalent geometry    : angle       0.60448 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 210
  time to evaluate  : 2.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7764 (mp0) cc_final: 0.7213 (mp0)
REVERT: A   92 ASP cc_start: 0.8534 (m-30) cc_final: 0.8284 (m-30)
REVERT: A  115 LYS cc_start: 0.9150 (mptt) cc_final: 0.8832 (mptt)
REVERT: B   32 TYR cc_start: 0.8225 (t80) cc_final: 0.7941 (t80)
REVERT: B   37 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8775 (mt)
REVERT: B   53 MET cc_start: 0.8306 (tpt) cc_final: 0.7989 (tpt)
REVERT: B  118 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8957 (pt)
REVERT: C   53 MET cc_start: 0.8275 (tpt) cc_final: 0.7959 (tpt)
REVERT: D   18 GLU cc_start: 0.7768 (mp0) cc_final: 0.7208 (mp0)
REVERT: D   92 ASP cc_start: 0.8545 (m-30) cc_final: 0.8296 (m-30)
REVERT: D  115 LYS cc_start: 0.9139 (mptt) cc_final: 0.8819 (mptt)
REVERT: E   32 TYR cc_start: 0.8244 (t80) cc_final: 0.7957 (t80)
REVERT: E   37 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8775 (mt)
REVERT: E   53 MET cc_start: 0.8288 (tpt) cc_final: 0.7986 (tpt)
REVERT: E  118 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8954 (pt)
REVERT: F   53 MET cc_start: 0.8270 (tpt) cc_final: 0.7953 (tpt)
REVERT: b  118 GLN cc_start: 0.9108 (tp-100) cc_final: 0.7234 (pm20)
REVERT: b  163 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8561 (mt-10)
REVERT: c   62 MET cc_start: 0.8265 (mtp) cc_final: 0.6880 (tpt)
REVERT: c  118 GLN cc_start: 0.9109 (tp-100) cc_final: 0.7184 (pm20)
REVERT: e  118 GLN cc_start: 0.9092 (tp-100) cc_final: 0.7223 (pm20)
REVERT: e  163 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8541 (mt-10)
REVERT: f   62 MET cc_start: 0.8113 (mtp) cc_final: 0.6886 (tpt)
  outliers start: 63
  outliers final: 42
  residues processed: 263
  average time/residue: 0.3056
  time to fit residues: 119.3589
Evaluate side-chains
  255 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 207
  time to evaluate  : 1.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  113 ASN
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain b residue  163 GLU
Chi-restraints excluded: chain b residue  230 LEU
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain e residue  163 GLU
Chi-restraints excluded: chain e residue  230 LEU
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 48 optimal weight:   30.0000
   chunk 181 optimal weight:   10.0000
   chunk 149 optimal weight:    0.0030
   chunk 203 optimal weight:    0.8980
   chunk 41 optimal weight:   20.0000
   chunk 220 optimal weight:    0.9980
   chunk 202 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 150 optimal weight:    3.9990
   chunk 157 optimal weight:    7.9990
   overall best weight:    2.1794

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

Flipped N/Q/H residues before XYZ refinement:
** a  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.072565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.063888 restraints weight = 62496.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 3.39
r_work: 0.3027 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18174  Z= 0.124
  Angle     :  0.581   7.954  24774  Z= 0.291
  Chirality :  0.049   0.214   2922
  Planarity :  0.004   0.040   3174
  Dihedral  :  4.400  25.255   2392
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.51 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.19), residues: 2202
  helix:  0.97 (0.31), residues: 258
  sheet: -0.50 (0.21), residues: 516
  loop : -0.18 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  90 
 HIS   0.002   0.001   HIS a  95 
 PHE   0.007   0.001   PHE c 171 
 TYR   0.025   0.001   TYR F 120 
 ARG   0.004   0.000   ARG C  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03510 (  396)
  hydrogen bonds       : angle       5.31187 (  918)
  covalent geometry    : bond        0.00297 (18174)
  covalent geometry    : angle       0.58150 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 221
  time to evaluate  : 2.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7711 (mp0) cc_final: 0.7155 (mp0)
REVERT: B   18 GLU cc_start: 0.7700 (mp0) cc_final: 0.7100 (mp0)
REVERT: B   32 TYR cc_start: 0.8157 (t80) cc_final: 0.7815 (t80)
REVERT: B   53 MET cc_start: 0.8273 (tpt) cc_final: 0.7958 (tpt)
REVERT: B  118 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8935 (pt)
REVERT: C   18 GLU cc_start: 0.7817 (mp0) cc_final: 0.7044 (mp0)
REVERT: C   53 MET cc_start: 0.8153 (tpt) cc_final: 0.7881 (tpt)
REVERT: D   18 GLU cc_start: 0.7704 (mp0) cc_final: 0.7143 (mp0)
REVERT: E   18 GLU cc_start: 0.7709 (mp0) cc_final: 0.7103 (mp0)
REVERT: E   32 TYR cc_start: 0.8174 (t80) cc_final: 0.7829 (t80)
REVERT: E   53 MET cc_start: 0.8314 (tpt) cc_final: 0.8029 (tpt)
REVERT: E  118 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8946 (pt)
REVERT: F   18 GLU cc_start: 0.7817 (mp0) cc_final: 0.7047 (mp0)
REVERT: F   53 MET cc_start: 0.8136 (tpt) cc_final: 0.7883 (tpt)
REVERT: b   62 MET cc_start: 0.8355 (ttm) cc_final: 0.6800 (tpt)
REVERT: b  118 GLN cc_start: 0.9041 (tp-100) cc_final: 0.7194 (pm20)
REVERT: b  163 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8539 (mt-10)
REVERT: c   62 MET cc_start: 0.7913 (mtp) cc_final: 0.6774 (tpt)
REVERT: c  118 GLN cc_start: 0.9026 (tp-100) cc_final: 0.7096 (pm20)
REVERT: e   62 MET cc_start: 0.8356 (ttm) cc_final: 0.6802 (tpt)
REVERT: e  118 GLN cc_start: 0.9013 (tp-100) cc_final: 0.7225 (pm20)
REVERT: e  163 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8525 (mt-10)
REVERT: f   62 MET cc_start: 0.7903 (mtp) cc_final: 0.6940 (tpt)
REVERT: f  118 GLN cc_start: 0.9025 (tp-100) cc_final: 0.7099 (pm20)
  outliers start: 50
  outliers final: 42
  residues processed: 261
  average time/residue: 0.3031
  time to fit residues: 118.8487
Evaluate side-chains
  267 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 221
  time to evaluate  : 1.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  113 ASN
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain b residue  163 GLU
Chi-restraints excluded: chain b residue  230 LEU
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain e residue  163 GLU
Chi-restraints excluded: chain e residue  230 LEU
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 201 optimal weight:    6.9990
   chunk 147 optimal weight:    6.9990
   chunk 172 optimal weight:   20.0000
   chunk 206 optimal weight:    9.9990
   chunk 146 optimal weight:    0.6980
   chunk 17 optimal weight:   20.0000
   chunk 109 optimal weight:    8.9990
   chunk 215 optimal weight:    0.9990
   chunk 204 optimal weight:   20.0000
   chunk 124 optimal weight:    0.0570
   overall best weight:    3.1504

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

Flipped N/Q/H residues before XYZ refinement:
** a  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.072104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.063441 restraints weight = 62466.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.37
r_work: 0.3018 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18174  Z= 0.139
  Angle     :  0.581   7.774  24774  Z= 0.289
  Chirality :  0.048   0.202   2922
  Planarity :  0.004   0.040   3174
  Dihedral  :  4.398  25.566   2392
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.65 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.19), residues: 2202
  helix:  0.98 (0.31), residues: 258
  sheet: -0.53 (0.21), residues: 516
  loop : -0.16 (0.19), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP a 184 
 HIS   0.003   0.001   HIS a  14 
 PHE   0.010   0.001   PHE B  85 
 TYR   0.023   0.001   TYR B 120 
 ARG   0.006   0.000   ARG C  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03436 (  396)
  hydrogen bonds       : angle       5.22600 (  918)
  covalent geometry    : bond        0.00336 (18174)
  covalent geometry    : angle       0.58084 (24774)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 218
  time to evaluate  : 2.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9173 (mptt) cc_final: 0.8842 (mptt)
REVERT: B   18 GLU cc_start: 0.7651 (mp0) cc_final: 0.7014 (mp0)
REVERT: B   32 TYR cc_start: 0.8164 (t80) cc_final: 0.7822 (t80)
REVERT: B   53 MET cc_start: 0.8266 (tpt) cc_final: 0.7961 (tpt)
REVERT: B  118 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8908 (pt)
REVERT: C   18 GLU cc_start: 0.7705 (mp0) cc_final: 0.6860 (mp0)
REVERT: C   53 MET cc_start: 0.8158 (tpt) cc_final: 0.7896 (tpt)
REVERT: D  115 LYS cc_start: 0.9173 (mptt) cc_final: 0.8843 (mptt)
REVERT: E   18 GLU cc_start: 0.7655 (mp0) cc_final: 0.7016 (mp0)
REVERT: E   32 TYR cc_start: 0.8189 (t80) cc_final: 0.7841 (t80)
REVERT: E   53 MET cc_start: 0.8304 (tpt) cc_final: 0.8019 (tpt)
REVERT: E  118 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8912 (pt)
REVERT: F   18 GLU cc_start: 0.7696 (mp0) cc_final: 0.6850 (mp0)
REVERT: F   53 MET cc_start: 0.8152 (tpt) cc_final: 0.7893 (tpt)
REVERT: b  118 GLN cc_start: 0.9036 (tp-100) cc_final: 0.7195 (pm20)
REVERT: b  163 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8565 (mt-10)
REVERT: c   62 MET cc_start: 0.8095 (mtp) cc_final: 0.6835 (tpt)
REVERT: c  118 GLN cc_start: 0.9061 (tp-100) cc_final: 0.7110 (pm20)
REVERT: e  118 GLN cc_start: 0.9023 (tp-100) cc_final: 0.7229 (pm20)
REVERT: e  163 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8556 (mt-10)
REVERT: f   62 MET cc_start: 0.8024 (mtp) cc_final: 0.6841 (tpt)
REVERT: f  118 GLN cc_start: 0.9062 (tp-100) cc_final: 0.7109 (pm20)
  outliers start: 44
  outliers final: 38
  residues processed: 252
  average time/residue: 0.3072
  time to fit residues: 115.8900
Evaluate side-chains
  253 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 211
  time to evaluate  : 2.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   76 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain C residue   46 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  113 ASN
Chi-restraints excluded: chain D residue  123 ILE
Chi-restraints excluded: chain E residue   41 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain a residue   36 VAL
Chi-restraints excluded: chain a residue  230 LEU
Chi-restraints excluded: chain b residue   36 VAL
Chi-restraints excluded: chain b residue  163 GLU
Chi-restraints excluded: chain b residue  230 LEU
Chi-restraints excluded: chain c residue   36 VAL
Chi-restraints excluded: chain c residue   82 ILE
Chi-restraints excluded: chain d residue   36 VAL
Chi-restraints excluded: chain d residue  230 LEU
Chi-restraints excluded: chain e residue   36 VAL
Chi-restraints excluded: chain e residue  163 GLU
Chi-restraints excluded: chain e residue  230 LEU
Chi-restraints excluded: chain f residue   36 VAL
Chi-restraints excluded: chain f residue   82 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 198 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 150 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 83 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9990
   chunk 144 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 180 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** a  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** f  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.071641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.063024 restraints weight = 62896.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 3.38
r_work: 0.3008 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  18174  Z= 0.156
  Angle     :  0.591   8.012  24774  Z= 0.294
  Chirality :  0.049   0.209   2922
  Planarity :  0.004   0.039   3174
  Dihedral  :  4.423  26.468   2392
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.32 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.19), residues: 2202
  helix:  0.98 (0.31), residues: 258
  sheet: -0.59 (0.21), residues: 516
  loop : -0.18 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP d 184 
 HIS   0.004   0.001   HIS d  14 
 PHE   0.007   0.001   PHE a 171 
 TYR   0.023   0.001   TYR B 120 
 ARG   0.005   0.000   ARG C  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  396)
  hydrogen bonds       : angle       5.18698 (  918)
  covalent geometry    : bond        0.00376 (18174)
  covalent geometry    : angle       0.59102 (24774)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7133.59 seconds
wall clock time: 124 minutes 58.63 seconds (7498.63 seconds total)