Starting phenix.real_space_refine
on Sun Jun 15 13:26:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kef_37154/06_2025/8kef_37154_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kef_37154/06_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_37154/06_2025/8kef_37154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kef_37154/06_2025/8kef_37154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kef_37154/06_2025/8kef_37154_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kef_37154/06_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-5710/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: 6.32, per 1000 atoms: 0.36
  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: 4.59
  Conformation dependent library (CDL) restraints added in 2.2 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: 1.95
  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: 5.02

  Time building geometry restraints manager: 5.33 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 D   3 "
           pdb=" C   TYR D   3 "
           pdb=" CA  TYR D   3 "
           pdb=" CB  TYR D   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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.700
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     35.720
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.500
-------------------------------------------------------------------------------
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  : 2.262 
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: 0.3090
  time to fit residues: 155.6863
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  : 2.250 
-------------------------------------------------------------------------------
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 = 0.073004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.064285 restraints weight = 62756.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 3.44
r_work: 0.3030 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
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  : 1.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.8322 (tpt) cc_final: 0.7871 (tpt)
REVERT: B   72 TYR cc_start: 0.8967 (t80) cc_final: 0.8747 (t80)
REVERT: C   53 MET cc_start: 0.8398 (tpt) cc_final: 0.7833 (tpt)
REVERT: E   53 MET cc_start: 0.8356 (tpt) cc_final: 0.7906 (tpt)
REVERT: E   72 TYR cc_start: 0.8980 (t80) cc_final: 0.8764 (t80)
REVERT: F   53 MET cc_start: 0.8388 (tpt) cc_final: 0.7823 (tpt)
REVERT: f   16 ASN cc_start: 0.7660 (t0) cc_final: 0.7398 (t0)
  outliers start: 32
  outliers final: 23
  residues processed: 244
  average time/residue: 0.3340
  time to fit residues: 123.0871
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  : 2.169 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 200 optimal weight:    8.9990
   chunk 115 optimal weight:    6.9990
   chunk 179 optimal weight:    5.9990
   chunk 166 optimal weight:    1.9990
   chunk 92 optimal weight:    0.2980
   chunk 56 optimal weight:   30.0000
   chunk 69 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 216 optimal weight:    8.9990
   chunk 204 optimal weight:    5.9990
   overall best weight:    3.4588

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.072748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.064163 restraints weight = 62697.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 3.34
r_work: 0.3032 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18174  Z= 0.139
  Angle     :  0.577   7.396  24774  Z= 0.292
  Chirality :  0.048   0.179   2922
  Planarity :  0.005   0.050   3174
  Dihedral  :  4.635  20.290   2392
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.49 %
    Favored  : 77.11 %
  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: -0.10 (0.18), residues: 2202
  helix:  1.05 (0.31), residues: 258
  sheet: -0.22 (0.22), residues: 516
  loop : -0.15 (0.18), residues: 1428

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   0.011   0.001   PHE c  78 
 TYR   0.012   0.001   TYR D 120 
 ARG   0.002   0.000   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04120 (  396)
  hydrogen bonds       : angle       5.76088 (  918)
  covalent geometry    : bond        0.00327 (18174)
  covalent geometry    : angle       0.57748 (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
  300 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 229
  time to evaluate  : 2.063 
Fit side-chains
REVERT: A   92 ASP cc_start: 0.8576 (m-30) cc_final: 0.8348 (m-30)
REVERT: B   53 MET cc_start: 0.8283 (tpt) cc_final: 0.7822 (tpt)
REVERT: B  121 ASP cc_start: 0.8180 (t0) cc_final: 0.7969 (t0)
REVERT: C   18 GLU cc_start: 0.7807 (mp0) cc_final: 0.7234 (mp0)
REVERT: C   53 MET cc_start: 0.8307 (tpt) cc_final: 0.7759 (tpt)
REVERT: D   92 ASP cc_start: 0.8580 (m-30) cc_final: 0.8355 (m-30)
REVERT: E   53 MET cc_start: 0.8305 (tpt) cc_final: 0.7841 (tpt)
REVERT: E  121 ASP cc_start: 0.8189 (t0) cc_final: 0.7979 (t0)
REVERT: F   18 GLU cc_start: 0.7801 (mp0) cc_final: 0.7234 (mp0)
REVERT: F   53 MET cc_start: 0.8302 (tpt) cc_final: 0.7754 (tpt)
REVERT: b  118 GLN cc_start: 0.9068 (tp-100) cc_final: 0.7199 (pm20)
REVERT: c   62 MET cc_start: 0.8400 (mtp) cc_final: 0.6788 (tpt)
REVERT: e  118 GLN cc_start: 0.9064 (tp-100) cc_final: 0.7193 (pm20)
REVERT: f   62 MET cc_start: 0.8394 (mtp) cc_final: 0.6816 (tpt)
  outliers start: 71
  outliers final: 41
  residues processed: 280
  average time/residue: 0.3032
  time to fit residues: 128.5664
Evaluate side-chains
  250 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 209
  time to evaluate  : 2.010 
-------------------------------------------------------------------------------
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 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 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:    2.9990
   chunk 194 optimal weight:   10.0000
   chunk 68 optimal weight:    8.9990
   chunk 95 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 100 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 215 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 56 optimal weight:   20.0000
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 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 = 0.3347 r_free = 0.3347 target = 0.073979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.065295 restraints weight = 62051.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 3.39
r_work: 0.3059 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  18174  Z= 0.109
  Angle     :  0.563   7.364  24774  Z= 0.284
  Chirality :  0.049   0.177   2922
  Planarity :  0.005   0.044   3174
  Dihedral  :  4.482  26.209   2392
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.83 %
    Favored  : 76.25 %
  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:  1.03 (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   0.006   0.001   TRP F  90 
 HIS   0.002   0.001   HIS a  95 
 PHE   0.009   0.001   PHE a  78 
 TYR   0.012   0.001   TYR E 120 
 ARG   0.006   0.000   ARG F 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  396)
  hydrogen bonds       : angle       5.65924 (  918)
  covalent geometry    : bond        0.00251 (18174)
  covalent geometry    : angle       0.56344 (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
  290 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 229
  time to evaluate  : 1.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8114 (tpt) cc_final: 0.7701 (tpt)
REVERT: A   66 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8694 (pt)
REVERT: A   92 ASP cc_start: 0.8551 (m-30) cc_final: 0.8261 (m-30)
REVERT: B   53 MET cc_start: 0.8221 (tpt) cc_final: 0.7707 (tpt)
REVERT: C   53 MET cc_start: 0.8168 (tpt) cc_final: 0.7627 (tpt)
REVERT: D   18 GLU cc_start: 0.7843 (mp0) cc_final: 0.7275 (mp0)
REVERT: D   53 MET cc_start: 0.8095 (tpt) cc_final: 0.7698 (tpt)
REVERT: D   66 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8711 (pt)
REVERT: D   92 ASP cc_start: 0.8549 (m-30) cc_final: 0.8259 (m-30)
REVERT: E   53 MET cc_start: 0.8256 (tpt) cc_final: 0.7742 (tpt)
REVERT: F   53 MET cc_start: 0.8183 (tpt) cc_final: 0.7642 (tpt)
REVERT: a    1 MET cc_start: 0.6396 (mpp) cc_final: 0.5951 (mtp)
REVERT: b   16 ASN cc_start: 0.7749 (t0) cc_final: 0.7482 (t0)
REVERT: b   62 MET cc_start: 0.8382 (mtp) cc_final: 0.6887 (tpt)
REVERT: b  118 GLN cc_start: 0.8996 (tp-100) cc_final: 0.7010 (pm20)
REVERT: c   62 MET cc_start: 0.8417 (mtp) cc_final: 0.6802 (tpt)
REVERT: d    1 MET cc_start: 0.6405 (mpp) cc_final: 0.5959 (mtp)
REVERT: e   16 ASN cc_start: 0.7752 (t0) cc_final: 0.7485 (t0)
REVERT: e   62 MET cc_start: 0.8368 (mtp) cc_final: 0.6880 (tpt)
REVERT: e  118 GLN cc_start: 0.8989 (tp-100) cc_final: 0.7002 (pm20)
REVERT: f   62 MET cc_start: 0.8326 (mtp) cc_final: 0.6672 (tpt)
  outliers start: 61
  outliers final: 44
  residues processed: 276
  average time/residue: 0.3012
  time to fit residues: 126.0009
Evaluate side-chains
  261 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 215
  time to evaluate  : 2.008 
-------------------------------------------------------------------------------
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   66 ILE
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   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   66 ILE
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:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 129 optimal weight:   30.0000
   chunk 50 optimal weight:   30.0000
   chunk 200 optimal weight:    5.9990
   chunk 125 optimal weight:    0.0370
   chunk 151 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 171 optimal weight:    8.9990
   overall best weight:    4.4066

-------------------------------------------------------------------------------
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 = 0.3311 r_free = 0.3311 target = 0.072322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.063715 restraints weight = 63294.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 3.40
r_work: 0.3013 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  18174  Z= 0.166
  Angle     :  0.586   7.370  24774  Z= 0.293
  Chirality :  0.049   0.195   2922
  Planarity :  0.004   0.043   3174
  Dihedral  :  4.463  25.190   2391
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.45 %
    Favored  : 76.25 %
  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:  0.85 (0.31), residues: 258
  sheet: -0.40 (0.21), residues: 516
  loop : -0.12 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  90 
 HIS   0.004   0.002   HIS d  14 
 PHE   0.008   0.001   PHE c 171 
 TYR   0.009   0.001   TYR E   3 
 ARG   0.003   0.000   ARG D 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  396)
  hydrogen bonds       : angle       5.53110 (  918)
  covalent geometry    : bond        0.00394 (18174)
  covalent geometry    : angle       0.58556 (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: 69
    poor density    : 217
  time to evaluate  : 2.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7845 (mp0) cc_final: 0.7285 (mp0)
REVERT: A   53 MET cc_start: 0.8123 (tpt) cc_final: 0.7821 (tpt)
REVERT: A   92 ASP cc_start: 0.8551 (m-30) cc_final: 0.8311 (m-30)
REVERT: B   18 GLU cc_start: 0.7735 (mp0) cc_final: 0.7101 (mp0)
REVERT: B   53 MET cc_start: 0.8297 (tpt) cc_final: 0.7860 (tpt)
REVERT: C   18 GLU cc_start: 0.7735 (mp0) cc_final: 0.7076 (mp0)
REVERT: C   53 MET cc_start: 0.8208 (tpt) cc_final: 0.7746 (tpt)
REVERT: D   53 MET cc_start: 0.8118 (tpt) cc_final: 0.7819 (tpt)
REVERT: D   92 ASP cc_start: 0.8555 (m-30) cc_final: 0.8318 (m-30)
REVERT: E   18 GLU cc_start: 0.7749 (mp0) cc_final: 0.7118 (mp0)
REVERT: E   53 MET cc_start: 0.8335 (tpt) cc_final: 0.7900 (tpt)
REVERT: F   18 GLU cc_start: 0.7740 (mp0) cc_final: 0.7087 (mp0)
REVERT: F   53 MET cc_start: 0.8191 (tpt) cc_final: 0.7729 (tpt)
REVERT: b  118 GLN cc_start: 0.9081 (tp-100) cc_final: 0.7201 (pm20)
REVERT: e  118 GLN cc_start: 0.9085 (tp-100) cc_final: 0.7204 (pm20)
  outliers start: 69
  outliers final: 44
  residues processed: 268
  average time/residue: 0.3145
  time to fit residues: 127.8742
Evaluate side-chains
  247 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 203
  time to evaluate  : 2.316 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
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:    0.7980
   chunk 136 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 137 optimal weight:    5.9990
   chunk 71 optimal weight:   20.0000
   chunk 113 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   overall best weight:    3.9588

-------------------------------------------------------------------------------
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**
** 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**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.071992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.063266 restraints weight = 62262.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 3.46
r_work: 0.3002 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  18174  Z= 0.150
  Angle     :  0.575   8.065  24774  Z= 0.286
  Chirality :  0.048   0.188   2922
  Planarity :  0.004   0.043   3174
  Dihedral  :  4.454  25.908   2391
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.12 %
    Favored  : 75.62 %
  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 (0.18), residues: 2202
  helix:  0.92 (0.31), residues: 258
  sheet: -0.53 (0.21), residues: 516
  loop : -0.14 (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 a  14 
 PHE   0.008   0.001   PHE c  78 
 TYR   0.010   0.001   TYR d 117 
 ARG   0.003   0.000   ARG F  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  396)
  hydrogen bonds       : angle       5.34943 (  918)
  covalent geometry    : bond        0.00361 (18174)
  covalent geometry    : angle       0.57516 (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
  291 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 223
  time to evaluate  : 2.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8142 (tpt) cc_final: 0.7845 (tpt)
REVERT: B   32 TYR cc_start: 0.8153 (t80) cc_final: 0.7890 (t80)
REVERT: B   53 MET cc_start: 0.8288 (tpt) cc_final: 0.7891 (tpt)
REVERT: C   53 MET cc_start: 0.8241 (tpt) cc_final: 0.7822 (tpt)
REVERT: D   18 GLU cc_start: 0.7775 (mp0) cc_final: 0.7162 (mp0)
REVERT: D   53 MET cc_start: 0.8151 (tpt) cc_final: 0.7856 (tpt)
REVERT: E   32 TYR cc_start: 0.8168 (t80) cc_final: 0.7901 (t80)
REVERT: E   53 MET cc_start: 0.8303 (tpt) cc_final: 0.7899 (tpt)
REVERT: F   53 MET cc_start: 0.8231 (tpt) cc_final: 0.7813 (tpt)
REVERT: b    1 MET cc_start: 0.6482 (mpp) cc_final: 0.6191 (mtt)
REVERT: b  118 GLN cc_start: 0.9086 (tp-100) cc_final: 0.7204 (pm20)
REVERT: b  163 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8556 (mt-10)
REVERT: c   62 MET cc_start: 0.8310 (mtp) cc_final: 0.6722 (tpt)
REVERT: e    1 MET cc_start: 0.6489 (mpp) cc_final: 0.6197 (mtt)
REVERT: e  118 GLN cc_start: 0.9096 (tp-100) cc_final: 0.7230 (pm20)
REVERT: e  163 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8547 (mt-10)
REVERT: f    1 MET cc_start: 0.6625 (mpp) cc_final: 0.6294 (mtt)
REVERT: f   62 MET cc_start: 0.8230 (mtp) cc_final: 0.6661 (tpt)
  outliers start: 68
  outliers final: 40
  residues processed: 281
  average time/residue: 0.3091
  time to fit residues: 129.1179
Evaluate side-chains
  261 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 219
  time to evaluate  : 1.997 
-------------------------------------------------------------------------------
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 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 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 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 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:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 209 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 154 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 159 optimal weight:    2.9990
   chunk 141 optimal weight:    5.9990
   chunk 213 optimal weight:   20.0000
   chunk 133 optimal weight:    8.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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  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 = 0.3263 r_free = 0.3263 target = 0.070290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.061686 restraints weight = 63050.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 3.33
r_work: 0.2968 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  18174  Z= 0.216
  Angle     :  0.625   8.694  24774  Z= 0.310
  Chirality :  0.049   0.208   2922
  Planarity :  0.004   0.041   3174
  Dihedral  :  4.647  27.194   2391
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 20.69 %
    Favored  : 75.38 %
  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: -0.32 (0.18), residues: 2202
  helix:  0.78 (0.31), residues: 258
  sheet: -0.67 (0.20), residues: 516
  loop : -0.14 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  90 
 HIS   0.004   0.001   HIS d  14 
 PHE   0.008   0.001   PHE f 171 
 TYR   0.019   0.001   TYR B 120 
 ARG   0.005   0.000   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  396)
  hydrogen bonds       : angle       5.43539 (  918)
  covalent geometry    : bond        0.00513 (18174)
  covalent geometry    : angle       0.62506 (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
  283 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 201
  time to evaluate  : 1.988 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.7770 (mp0) cc_final: 0.7218 (mp0)
REVERT: A  115 LYS cc_start: 0.9147 (mptt) cc_final: 0.8830 (mptt)
REVERT: B   18 GLU cc_start: 0.7755 (mp0) cc_final: 0.7138 (mp0)
REVERT: B   32 TYR cc_start: 0.8263 (t80) cc_final: 0.7895 (t80)
REVERT: B   53 MET cc_start: 0.8363 (tpt) cc_final: 0.8043 (tpt)
REVERT: B  118 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8993 (pt)
REVERT: C   18 GLU cc_start: 0.7797 (mp0) cc_final: 0.7185 (mp0)
REVERT: C   53 MET cc_start: 0.8318 (tpt) cc_final: 0.8001 (tpt)
REVERT: E   18 GLU cc_start: 0.7753 (mp0) cc_final: 0.7133 (mp0)
REVERT: E   32 TYR cc_start: 0.8279 (t80) cc_final: 0.7909 (t80)
REVERT: E   53 MET cc_start: 0.8388 (tpt) cc_final: 0.8067 (tpt)
REVERT: E  118 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9021 (pt)
REVERT: F   18 GLU cc_start: 0.7771 (mp0) cc_final: 0.7164 (mp0)
REVERT: F   53 MET cc_start: 0.8283 (tpt) cc_final: 0.7963 (tpt)
REVERT: b    1 MET cc_start: 0.6742 (mpp) cc_final: 0.6258 (mtt)
REVERT: b  118 GLN cc_start: 0.9117 (tp-100) cc_final: 0.7240 (pm20)
REVERT: b  163 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8440 (mt-10)
REVERT: c    1 MET cc_start: 0.6717 (mpp) cc_final: 0.6345 (mtt)
REVERT: c   62 MET cc_start: 0.8220 (mtp) cc_final: 0.6904 (tpt)
REVERT: e    1 MET cc_start: 0.6752 (mpp) cc_final: 0.6266 (mtt)
REVERT: e  118 GLN cc_start: 0.9115 (tp-100) cc_final: 0.7236 (pm20)
REVERT: e  163 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8426 (mt-10)
REVERT: f   62 MET cc_start: 0.8201 (mtp) cc_final: 0.6890 (tpt)
  outliers start: 82
  outliers final: 44
  residues processed: 277
  average time/residue: 0.3326
  time to fit residues: 138.1900
Evaluate side-chains
  245 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 197
  time to evaluate  : 2.061 
-------------------------------------------------------------------------------
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  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   74 THR
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  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   74 THR
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  146 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 e residue   36 VAL
Chi-restraints excluded: chain e residue  146 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 157 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 153 optimal weight:   20.0000
   chunk 154 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 207 optimal weight:    0.0000
   chunk 3 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 199 optimal weight:    0.7980
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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  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 = 0.3305 r_free = 0.3305 target = 0.072134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.063558 restraints weight = 61936.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.38
r_work: 0.3012 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18174  Z= 0.127
  Angle     :  0.583   8.214  24774  Z= 0.291
  Chirality :  0.049   0.193   2922
  Planarity :  0.004   0.040   3174
  Dihedral  :  4.523  28.561   2391
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.79 %
    Favored  : 75.67 %
  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: -0.30 (0.19), residues: 2202
  helix:  0.94 (0.31), residues: 258
  sheet: -0.61 (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 b 184 
 HIS   0.002   0.001   HIS d  95 
 PHE   0.007   0.001   PHE c 171 
 TYR   0.028   0.001   TYR E 120 
 ARG   0.004   0.000   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  396)
  hydrogen bonds       : angle       5.36239 (  918)
  covalent geometry    : bond        0.00311 (18174)
  covalent geometry    : angle       0.58345 (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
  279 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 226
  time to evaluate  : 2.236 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.7739 (mp0) cc_final: 0.7177 (mp0)
REVERT: A   26 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8904 (mtpp)
REVERT: A   53 MET cc_start: 0.8191 (tpt) cc_final: 0.7879 (tpt)
REVERT: B   18 GLU cc_start: 0.7759 (mp0) cc_final: 0.7103 (mp0)
REVERT: B   32 TYR cc_start: 0.8205 (t80) cc_final: 0.7866 (t80)
REVERT: B   53 MET cc_start: 0.8256 (tpt) cc_final: 0.7975 (tpt)
REVERT: B  118 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8965 (pt)
REVERT: C   53 MET cc_start: 0.8281 (tpt) cc_final: 0.8002 (tpt)
REVERT: D   18 GLU cc_start: 0.7718 (mp0) cc_final: 0.7124 (mp0)
REVERT: D   26 LYS cc_start: 0.9178 (mtpp) cc_final: 0.8904 (mtpp)
REVERT: D   53 MET cc_start: 0.8188 (tpt) cc_final: 0.7878 (tpt)
REVERT: D  115 LYS cc_start: 0.9168 (mptt) cc_final: 0.8892 (mptt)
REVERT: E   18 GLU cc_start: 0.7699 (mp0) cc_final: 0.7029 (mp0)
REVERT: E   32 TYR cc_start: 0.8184 (t80) cc_final: 0.7843 (t80)
REVERT: E   53 MET cc_start: 0.8303 (tpt) cc_final: 0.8019 (tpt)
REVERT: E  118 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8986 (pt)
REVERT: F   53 MET cc_start: 0.8270 (tpt) cc_final: 0.7992 (tpt)
REVERT: b    1 MET cc_start: 0.6572 (mpp) cc_final: 0.6135 (mtt)
REVERT: b   62 MET cc_start: 0.8192 (mtp) cc_final: 0.6375 (tpt)
REVERT: b  118 GLN cc_start: 0.9033 (tp-100) cc_final: 0.7169 (pm20)
REVERT: b  163 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8446 (mt-10)
REVERT: c    1 MET cc_start: 0.6862 (mpp) cc_final: 0.6472 (mtt)
REVERT: c   62 MET cc_start: 0.7915 (mtp) cc_final: 0.6759 (tpt)
REVERT: c  118 GLN cc_start: 0.9056 (tp-100) cc_final: 0.7116 (pm20)
REVERT: e    1 MET cc_start: 0.6568 (mpp) cc_final: 0.6139 (mtt)
REVERT: e   62 MET cc_start: 0.8195 (mtp) cc_final: 0.6369 (tpt)
REVERT: e  118 GLN cc_start: 0.9030 (tp-100) cc_final: 0.7167 (pm20)
REVERT: e  163 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8449 (mt-10)
REVERT: f    1 MET cc_start: 0.6622 (mpp) cc_final: 0.6189 (mtt)
REVERT: f   62 MET cc_start: 0.7908 (mtp) cc_final: 0.6756 (tpt)
REVERT: f  118 GLN cc_start: 0.9066 (tp-100) cc_final: 0.7119 (pm20)
  outliers start: 53
  outliers final: 40
  residues processed: 269
  average time/residue: 0.4074
  time to fit residues: 167.6385
Evaluate side-chains
  258 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 214
  time to evaluate  : 2.601 
-------------------------------------------------------------------------------
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  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  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 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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0570
   chunk 181 optimal weight:    9.9990
   chunk 149 optimal weight:    0.0570
   chunk 203 optimal weight:    8.9990
   chunk 41 optimal weight:   20.0000
   chunk 220 optimal weight:    0.6980
   chunk 202 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 150 optimal weight:    0.6980
   chunk 157 optimal weight:    8.9990
   overall best weight:    1.5018

-------------------------------------------------------------------------------
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 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.073087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.064468 restraints weight = 62119.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 3.37
r_work: 0.3042 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2736

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= 0.113
  Angle     :  0.569   7.880  24774  Z= 0.285
  Chirality :  0.048   0.172   2922
  Planarity :  0.004   0.041   3174
  Dihedral  :  4.363  27.590   2391
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 22.13 %
    Favored  : 75.62 %
  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:  1.03 (0.31), residues: 258
  sheet: -0.54 (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 a 184 
 HIS   0.002   0.001   HIS a  95 
 PHE   0.008   0.001   PHE B  85 
 TYR   0.026   0.001   TYR E 120 
 ARG   0.003   0.000   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03430 (  396)
  hydrogen bonds       : angle       5.36134 (  918)
  covalent geometry    : bond        0.00271 (18174)
  covalent geometry    : angle       0.56918 (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
  270 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 223
  time to evaluate  : 2.946 
Fit side-chains
REVERT: A   18 GLU cc_start: 0.7682 (mp0) cc_final: 0.7129 (mp0)
REVERT: A   26 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8927 (mtpp)
REVERT: A   53 MET cc_start: 0.8190 (tpt) cc_final: 0.7870 (tpt)
REVERT: B   32 TYR cc_start: 0.8145 (t80) cc_final: 0.7826 (t80)
REVERT: B   53 MET cc_start: 0.8264 (tpt) cc_final: 0.7962 (tpt)
REVERT: B  118 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8909 (pt)
REVERT: C   18 GLU cc_start: 0.7798 (mp0) cc_final: 0.7011 (mp0)
REVERT: C   53 MET cc_start: 0.8165 (tpt) cc_final: 0.7936 (tpt)
REVERT: D   18 GLU cc_start: 0.7707 (mp0) cc_final: 0.7138 (mp0)
REVERT: D   26 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8927 (mtpp)
REVERT: D   53 MET cc_start: 0.8180 (tpt) cc_final: 0.7874 (tpt)
REVERT: E   32 TYR cc_start: 0.8165 (t80) cc_final: 0.7843 (t80)
REVERT: E   53 MET cc_start: 0.8289 (tpt) cc_final: 0.7984 (tpt)
REVERT: E   75 ASP cc_start: 0.8811 (m-30) cc_final: 0.8608 (p0)
REVERT: E  118 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8912 (pt)
REVERT: F   18 GLU cc_start: 0.7773 (mp0) cc_final: 0.6992 (mp0)
REVERT: F   53 MET cc_start: 0.8150 (tpt) cc_final: 0.7919 (tpt)
REVERT: b    1 MET cc_start: 0.6300 (mpp) cc_final: 0.6022 (mtt)
REVERT: b   62 MET cc_start: 0.8186 (mtp) cc_final: 0.6477 (tpt)
REVERT: b  118 GLN cc_start: 0.8952 (tp-100) cc_final: 0.7183 (pm20)
REVERT: b  163 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8443 (mt-10)
REVERT: c    1 MET cc_start: 0.6399 (mpp) cc_final: 0.6180 (mtt)
REVERT: c   62 MET cc_start: 0.7686 (mtp) cc_final: 0.6612 (tpt)
REVERT: c  118 GLN cc_start: 0.9018 (tp-100) cc_final: 0.7063 (pm20)
REVERT: e    1 MET cc_start: 0.6305 (mpp) cc_final: 0.6031 (mtt)
REVERT: e   62 MET cc_start: 0.8186 (mtp) cc_final: 0.6470 (tpt)
REVERT: e  118 GLN cc_start: 0.8971 (tp-100) cc_final: 0.7213 (pm20)
REVERT: e  163 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8444 (mt-10)
REVERT: f    1 MET cc_start: 0.6270 (mpp) cc_final: 0.6014 (mtt)
REVERT: f   62 MET cc_start: 0.7699 (mtp) cc_final: 0.6620 (tpt)
REVERT: f  118 GLN cc_start: 0.9029 (tp-100) cc_final: 0.7084 (pm20)
  outliers start: 47
  outliers final: 35
  residues processed: 262
  average time/residue: 0.4218
  time to fit residues: 169.3893
Evaluate side-chains
  254 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 215
  time to evaluate  : 2.548 
-------------------------------------------------------------------------------
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  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  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 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 e residue   36 VAL
Chi-restraints excluded: chain e residue  163 GLU
Chi-restraints excluded: chain e residue  193 ILE
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=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:    0.7980
   chunk 206 optimal weight:   20.0000
   chunk 146 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 109 optimal weight:    9.9990
   chunk 215 optimal weight:    0.0050
   chunk 204 optimal weight:    9.9990
   chunk 124 optimal weight:    0.0870
   overall best weight:    1.9776

-------------------------------------------------------------------------------
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 ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.073061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.064494 restraints weight = 62069.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 3.37
r_work: 0.3041 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  18174  Z= 0.120
  Angle     :  0.574   7.606  24774  Z= 0.288
  Chirality :  0.048   0.183   2922
  Planarity :  0.005   0.071   3174
  Dihedral  :  4.300  27.179   2391
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.22 %
    Favored  : 75.67 %
  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: -0.26 (0.19), residues: 2202
  helix:  1.05 (0.32), residues: 258
  sheet: -0.55 (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 b 184 
 HIS   0.002   0.001   HIS a  95 
 PHE   0.006   0.001   PHE e 171 
 TYR   0.025   0.001   TYR B 120 
 ARG   0.004   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  396)
  hydrogen bonds       : angle       5.31181 (  918)
  covalent geometry    : bond        0.00291 (18174)
  covalent geometry    : angle       0.57399 (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
  269 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 225
  time to evaluate  : 2.043 
Fit side-chains
REVERT: A   12 LYS cc_start: 0.7103 (tmtt) cc_final: 0.6865 (tttm)
REVERT: A   18 GLU cc_start: 0.7705 (mp0) cc_final: 0.7162 (mp0)
REVERT: A   26 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8953 (mtpp)
REVERT: A   53 MET cc_start: 0.8179 (tpt) cc_final: 0.7858 (tpt)
REVERT: A  129 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: B   18 GLU cc_start: 0.7621 (mp0) cc_final: 0.6980 (mp0)
REVERT: B   32 TYR cc_start: 0.8197 (t80) cc_final: 0.7872 (t80)
REVERT: B   53 MET cc_start: 0.8269 (tpt) cc_final: 0.7975 (tpt)
REVERT: B  118 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8919 (pt)
REVERT: C   18 GLU cc_start: 0.7704 (mp0) cc_final: 0.6887 (mp0)
REVERT: C   53 MET cc_start: 0.8124 (tpt) cc_final: 0.7893 (tpt)
REVERT: D   12 LYS cc_start: 0.7099 (tmtt) cc_final: 0.6857 (tttm)
REVERT: D   18 GLU cc_start: 0.7721 (mp0) cc_final: 0.7166 (mp0)
REVERT: D   26 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8954 (mtpp)
REVERT: D   53 MET cc_start: 0.8176 (tpt) cc_final: 0.7861 (tpt)
REVERT: E   18 GLU cc_start: 0.7649 (mp0) cc_final: 0.7023 (mp0)
REVERT: E   32 TYR cc_start: 0.8201 (t80) cc_final: 0.7877 (t80)
REVERT: E   53 MET cc_start: 0.8287 (tpt) cc_final: 0.7996 (tpt)
REVERT: E  118 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8923 (pt)
REVERT: F   18 GLU cc_start: 0.7730 (mp0) cc_final: 0.6914 (mp0)
REVERT: F   53 MET cc_start: 0.8123 (tpt) cc_final: 0.7896 (tpt)
REVERT: b    1 MET cc_start: 0.6194 (mpp) cc_final: 0.5948 (mtt)
REVERT: b   62 MET cc_start: 0.8136 (mtp) cc_final: 0.6447 (tpt)
REVERT: b  118 GLN cc_start: 0.8964 (tp-100) cc_final: 0.7175 (pm20)
REVERT: b  163 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8478 (mt-10)
REVERT: c   62 MET cc_start: 0.7816 (mtp) cc_final: 0.6751 (tpt)
REVERT: c  118 GLN cc_start: 0.9022 (tp-100) cc_final: 0.7084 (pm20)
REVERT: e    1 MET cc_start: 0.6193 (mpp) cc_final: 0.5942 (mtt)
REVERT: e   62 MET cc_start: 0.8133 (mtp) cc_final: 0.6440 (tpt)
REVERT: e  118 GLN cc_start: 0.8966 (tp-100) cc_final: 0.7172 (pm20)
REVERT: e  163 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8465 (mt-10)
REVERT: f    1 MET cc_start: 0.6236 (mpp) cc_final: 0.5966 (mtt)
REVERT: f   62 MET cc_start: 0.7816 (mtp) cc_final: 0.6752 (tpt)
REVERT: f  118 GLN cc_start: 0.9024 (tp-100) cc_final: 0.7079 (pm20)
  outliers start: 44
  outliers final: 32
  residues processed: 258
  average time/residue: 0.3085
  time to fit residues: 119.0346
Evaluate side-chains
  254 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 218
  time to evaluate  : 2.012 
-------------------------------------------------------------------------------
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   76 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  123 ILE
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   76 VAL
Chi-restraints excluded: chain E residue  103 SER
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  123 ILE
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 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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 198 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 150 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 83 optimal weight:    0.2980
   chunk 78 optimal weight:    6.9990
   chunk 144 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 180 optimal weight:   20.0000
   chunk 63 optimal weight:    0.7980
   overall best weight:    3.6186

-------------------------------------------------------------------------------
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 = 0.3305 r_free = 0.3305 target = 0.071952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.063372 restraints weight = 62711.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 3.37
r_work: 0.3015 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  18174  Z= 0.150
  Angle     :  0.590   7.978  24774  Z= 0.295
  Chirality :  0.049   0.211   2922
  Planarity :  0.005   0.069   3174
  Dihedral  :  4.342  27.247   2391
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 22.61 %
    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: -0.30 (0.19), residues: 2202
  helix:  0.98 (0.32), residues: 258
  sheet: -0.59 (0.21), residues: 516
  loop : -0.20 (0.18), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP b 184 
 HIS   0.004   0.001   HIS a  14 
 PHE   0.010   0.001   PHE E  85 
 TYR   0.023   0.001   TYR E 120 
 ARG   0.004   0.000   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  396)
  hydrogen bonds       : angle       5.22935 (  918)
  covalent geometry    : bond        0.00363 (18174)
  covalent geometry    : angle       0.59016 (24774)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7437.36 seconds
wall clock time: 131 minutes 50.25 seconds (7910.25 seconds total)