Starting phenix.real_space_refine
on Fri May 16 04:25:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k36_36845/05_2025/8k36_36845.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k36_36845/05_2025/8k36_36845.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k36_36845/05_2025/8k36_36845.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k36_36845/05_2025/8k36_36845.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k36_36845/05_2025/8k36_36845.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k36_36845/05_2025/8k36_36845.cif"
  }
  resolution = 3.48
  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=   0.007
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      36      5.16       5
     C    8892      2.51       5
     N    2400      2.21       5
     O    2844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14172
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "B"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "C"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "D"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "E"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "F"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "G"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "H"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "I"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "J"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "K"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
    Chain: "L"
      Number of atoms: 1181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1181
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 9, 'TRANS': 144}
  Time building chain proxies: 8.75, per 1000 atoms: 0.62
  Number of scatterers: 14172
  At special positions: 0
  Unit cell: (110.16, 110.16, 108.8, 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      36     16.00
     O    2844      8.00
     N    2400      7.00
     C    8892      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.09
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3336

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 32 sheets defined
      9.5% alpha, 44.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.501A  pdb=" N   GLN A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 155
      removed outlier: 3.646A  pdb=" N   ARG A 155 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 102
    Processing helix  chain 'C' and resid 90 through 102
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 151 through 155
      removed outlier: 3.649A  pdb=" N   ARG D 155 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 102
    Processing helix  chain 'F' and resid 90 through 102
    Processing helix  chain 'G' and resid 90 through 102
      removed outlier: 3.500A  pdb=" N   GLN G  94 " --> pdb=" O   GLU G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 151 through 155
      removed outlier: 3.645A  pdb=" N   ARG G 155 " --> pdb=" O   ALA G 152 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'I' and resid 90 through 102
    Processing helix  chain 'J' and resid 90 through 102
    Processing helix  chain 'J' and resid 151 through 155
      removed outlier: 3.648A  pdb=" N   ARG J 155 " --> pdb=" O   ALA J 152 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 90 through 102
    Processing helix  chain 'L' and resid 90 through 102
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39
      removed outlier: 4.534A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   ALA A 107 " --> pdb=" O   TYR A  20 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LYS A 142 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ILE A 127 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   THR A 140 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   THR A 138 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   SER A  81 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   LEU A  45 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   THR A  83 " --> pdb=" O   LYS A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39
      removed outlier: 4.534A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   ALA A 107 " --> pdb=" O   TYR A  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51
      removed outlier: 5.269A  pdb=" N   ALA B 107 " --> pdb=" O   TYR B  20 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   LEU B  17 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51
      removed outlier: 5.161A  pdb=" N   VAL B 124 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   THR B 144 " --> pdb=" O   VAL B 124 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR B 138 " --> pdb=" O   ALA B 130 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   SER B  81 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LEU B  45 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   THR B  83 " --> pdb=" O   LYS B  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 56
    Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 76
      removed outlier: 5.817A  pdb=" N   GLU B  53 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LYS B  75 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   THR B  51 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   SER C 125 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
      removed outlier: 9.375A  pdb=" N   SER B  54 " --> pdb=" O   TRP C 123 " (cutoff:3.500A)
      removed outlier: 12.211A  pdb=" N   TRP C 123 " --> pdb=" O   SER B  54 " (cutoff:3.500A)
      removed outlier: 14.551A  pdb=" N   ASP B  56 " --> pdb=" O   ARG C 121 " (cutoff:3.500A)
      removed outlier: 18.179A  pdb=" N   ARG C 121 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   ALA C 107 " --> pdb=" O   TYR C  20 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LEU C  17 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 76
      removed outlier: 5.817A  pdb=" N   GLU B  53 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LYS B  75 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   THR B  51 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   SER C 125 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
      removed outlier: 9.375A  pdb=" N   SER B  54 " --> pdb=" O   TRP C 123 " (cutoff:3.500A)
      removed outlier: 12.211A  pdb=" N   TRP C 123 " --> pdb=" O   SER B  54 " (cutoff:3.500A)
      removed outlier: 14.551A  pdb=" N   ASP B  56 " --> pdb=" O   ARG C 121 " (cutoff:3.500A)
      removed outlier: 18.179A  pdb=" N   ARG C 121 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LYS C 142 " --> pdb=" O   SER C 125 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ILE C 127 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   THR C 140 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   LYS C 129 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   THR C 138 " --> pdb=" O   LYS C 129 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   SER C  81 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   LEU C  45 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR C  83 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51
      removed outlier: 5.345A  pdb=" N   ALA D 107 " --> pdb=" O   TYR D  20 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   LEU D  17 " --> pdb=" O   LEU D  39 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 51
      removed outlier: 6.565A  pdb=" N   LYS D 142 " --> pdb=" O   SER D 125 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ILE D 127 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   THR D 140 " --> pdb=" O   ILE D 127 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   LYS D 129 " --> pdb=" O   THR D 138 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   THR D 138 " --> pdb=" O   LYS D 129 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   SER D  81 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   LEU D  45 " --> pdb=" O   SER D  81 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   THR D  83 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 54 through 56
    Processing sheet with id=AB2, first strand: chain 'D' and resid 50 through 51
      removed outlier: 5.270A  pdb=" N   ALA E 107 " --> pdb=" O   TYR E  20 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   LEU E  17 " --> pdb=" O   LEU E  39 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51
      removed outlier: 5.160A  pdb=" N   VAL E 124 " --> pdb=" O   THR E 144 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   THR E 144 " --> pdb=" O   VAL E 124 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR E 138 " --> pdb=" O   ALA E 130 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   SER E  81 " --> pdb=" O   LEU E  45 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   LEU E  45 " --> pdb=" O   SER E  81 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   THR E  83 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 56
    Processing sheet with id=AB5, first strand: chain 'E' and resid 70 through 76
      removed outlier: 5.812A  pdb=" N   GLU E  53 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   LYS E  75 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   THR E  51 " --> pdb=" O   LYS E  75 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   SER F 125 " --> pdb=" O   ALA E  52 " (cutoff:3.500A)
      removed outlier: 9.377A  pdb=" N   SER E  54 " --> pdb=" O   TRP F 123 " (cutoff:3.500A)
      removed outlier: 12.214A  pdb=" N   TRP F 123 " --> pdb=" O   SER E  54 " (cutoff:3.500A)
      removed outlier: 14.548A  pdb=" N   ASP E  56 " --> pdb=" O   ARG F 121 " (cutoff:3.500A)
      removed outlier: 18.172A  pdb=" N   ARG F 121 " --> pdb=" O   ASP E  56 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   ALA F 107 " --> pdb=" O   TYR F  20 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   LEU F  17 " --> pdb=" O   LEU F  39 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 70 through 76
      removed outlier: 5.812A  pdb=" N   GLU E  53 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   LYS E  75 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   THR E  51 " --> pdb=" O   LYS E  75 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   SER F 125 " --> pdb=" O   ALA E  52 " (cutoff:3.500A)
      removed outlier: 9.377A  pdb=" N   SER E  54 " --> pdb=" O   TRP F 123 " (cutoff:3.500A)
      removed outlier: 12.214A  pdb=" N   TRP F 123 " --> pdb=" O   SER E  54 " (cutoff:3.500A)
      removed outlier: 14.548A  pdb=" N   ASP E  56 " --> pdb=" O   ARG F 121 " (cutoff:3.500A)
      removed outlier: 18.172A  pdb=" N   ARG F 121 " --> pdb=" O   ASP E  56 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LYS F 142 " --> pdb=" O   SER F 125 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ILE F 127 " --> pdb=" O   THR F 140 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR F 140 " --> pdb=" O   ILE F 127 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LYS F 129 " --> pdb=" O   THR F 138 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   THR F 138 " --> pdb=" O   LYS F 129 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER F  81 " --> pdb=" O   LEU F  45 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   LEU F  45 " --> pdb=" O   SER F  81 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   THR F  83 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 54 through 56
    Processing sheet with id=AB8, first strand: chain 'G' and resid 36 through 39
      removed outlier: 4.533A  pdb=" N   LEU G  17 " --> pdb=" O   LEU G  39 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ALA G 107 " --> pdb=" O   TYR G  20 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LYS G 142 " --> pdb=" O   SER G 125 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ILE G 127 " --> pdb=" O   THR G 140 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   THR G 140 " --> pdb=" O   ILE G 127 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LYS G 129 " --> pdb=" O   THR G 138 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   THR G 138 " --> pdb=" O   LYS G 129 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   SER G  81 " --> pdb=" O   LEU G  45 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   LEU G  45 " --> pdb=" O   SER G  81 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   THR G  83 " --> pdb=" O   LYS G  43 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 36 through 39
      removed outlier: 4.533A  pdb=" N   LEU G  17 " --> pdb=" O   LEU G  39 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ALA G 107 " --> pdb=" O   TYR G  20 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 50 through 51
      removed outlier: 5.270A  pdb=" N   ALA H 107 " --> pdb=" O   TYR H  20 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   LEU H  17 " --> pdb=" O   LEU H  39 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 50 through 51
      removed outlier: 5.162A  pdb=" N   VAL H 124 " --> pdb=" O   THR H 144 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   THR H 144 " --> pdb=" O   VAL H 124 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR H 138 " --> pdb=" O   ALA H 130 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   SER H  81 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LEU H  45 " --> pdb=" O   SER H  81 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   THR H  83 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 54 through 56
    Processing sheet with id=AC4, first strand: chain 'H' and resid 70 through 76
      removed outlier: 5.816A  pdb=" N   GLU H  53 " --> pdb=" O   GLY H  73 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LYS H  75 " --> pdb=" O   THR H  51 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   THR H  51 " --> pdb=" O   LYS H  75 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   SER I 125 " --> pdb=" O   ALA H  52 " (cutoff:3.500A)
      removed outlier: 9.376A  pdb=" N   SER H  54 " --> pdb=" O   TRP I 123 " (cutoff:3.500A)
      removed outlier: 12.212A  pdb=" N   TRP I 123 " --> pdb=" O   SER H  54 " (cutoff:3.500A)
      removed outlier: 14.552A  pdb=" N   ASP H  56 " --> pdb=" O   ARG I 121 " (cutoff:3.500A)
      removed outlier: 18.180A  pdb=" N   ARG I 121 " --> pdb=" O   ASP H  56 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ALA I 107 " --> pdb=" O   TYR I  20 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LEU I  17 " --> pdb=" O   LEU I  39 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 70 through 76
      removed outlier: 5.816A  pdb=" N   GLU H  53 " --> pdb=" O   GLY H  73 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LYS H  75 " --> pdb=" O   THR H  51 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   THR H  51 " --> pdb=" O   LYS H  75 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   SER I 125 " --> pdb=" O   ALA H  52 " (cutoff:3.500A)
      removed outlier: 9.376A  pdb=" N   SER H  54 " --> pdb=" O   TRP I 123 " (cutoff:3.500A)
      removed outlier: 12.212A  pdb=" N   TRP I 123 " --> pdb=" O   SER H  54 " (cutoff:3.500A)
      removed outlier: 14.552A  pdb=" N   ASP H  56 " --> pdb=" O   ARG I 121 " (cutoff:3.500A)
      removed outlier: 18.180A  pdb=" N   ARG I 121 " --> pdb=" O   ASP H  56 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LYS I 142 " --> pdb=" O   SER I 125 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ILE I 127 " --> pdb=" O   THR I 140 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   THR I 140 " --> pdb=" O   ILE I 127 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   LYS I 129 " --> pdb=" O   THR I 138 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   THR I 138 " --> pdb=" O   LYS I 129 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER I  81 " --> pdb=" O   LEU I  45 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   LEU I  45 " --> pdb=" O   SER I  81 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   THR I  83 " --> pdb=" O   LYS I  43 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'I' and resid 50 through 51
      removed outlier: 5.345A  pdb=" N   ALA J 107 " --> pdb=" O   TYR J  20 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   LEU J  17 " --> pdb=" O   LEU J  39 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'I' and resid 50 through 51
      removed outlier: 6.565A  pdb=" N   LYS J 142 " --> pdb=" O   SER J 125 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ILE J 127 " --> pdb=" O   THR J 140 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   THR J 140 " --> pdb=" O   ILE J 127 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   LYS J 129 " --> pdb=" O   THR J 138 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   THR J 138 " --> pdb=" O   LYS J 129 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   SER J  81 " --> pdb=" O   LEU J  45 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   LEU J  45 " --> pdb=" O   SER J  81 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   THR J  83 " --> pdb=" O   LYS J  43 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'I' and resid 54 through 56
    Processing sheet with id=AC9, first strand: chain 'J' and resid 50 through 51
      removed outlier: 5.270A  pdb=" N   ALA K 107 " --> pdb=" O   TYR K  20 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   LEU K  17 " --> pdb=" O   LEU K  39 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'J' and resid 50 through 51
      removed outlier: 5.160A  pdb=" N   VAL K 124 " --> pdb=" O   THR K 144 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   THR K 144 " --> pdb=" O   VAL K 124 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   THR K 138 " --> pdb=" O   ALA K 130 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   SER K  81 " --> pdb=" O   LEU K  45 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   LEU K  45 " --> pdb=" O   SER K  81 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   THR K  83 " --> pdb=" O   LYS K  43 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'J' and resid 54 through 56
    Processing sheet with id=AD3, first strand: chain 'K' and resid 70 through 76
      removed outlier: 5.811A  pdb=" N   GLU K  53 " --> pdb=" O   GLY K  73 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   LYS K  75 " --> pdb=" O   THR K  51 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   THR K  51 " --> pdb=" O   LYS K  75 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   SER L 125 " --> pdb=" O   ALA K  52 " (cutoff:3.500A)
      removed outlier: 9.376A  pdb=" N   SER K  54 " --> pdb=" O   TRP L 123 " (cutoff:3.500A)
      removed outlier: 12.213A  pdb=" N   TRP L 123 " --> pdb=" O   SER K  54 " (cutoff:3.500A)
      removed outlier: 14.546A  pdb=" N   ASP K  56 " --> pdb=" O   ARG L 121 " (cutoff:3.500A)
      removed outlier: 18.171A  pdb=" N   ARG L 121 " --> pdb=" O   ASP K  56 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ALA L 107 " --> pdb=" O   TYR L  20 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LEU L  17 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'K' and resid 70 through 76
      removed outlier: 5.811A  pdb=" N   GLU K  53 " --> pdb=" O   GLY K  73 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   LYS K  75 " --> pdb=" O   THR K  51 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   THR K  51 " --> pdb=" O   LYS K  75 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   SER L 125 " --> pdb=" O   ALA K  52 " (cutoff:3.500A)
      removed outlier: 9.376A  pdb=" N   SER K  54 " --> pdb=" O   TRP L 123 " (cutoff:3.500A)
      removed outlier: 12.213A  pdb=" N   TRP L 123 " --> pdb=" O   SER K  54 " (cutoff:3.500A)
      removed outlier: 14.546A  pdb=" N   ASP K  56 " --> pdb=" O   ARG L 121 " (cutoff:3.500A)
      removed outlier: 18.171A  pdb=" N   ARG L 121 " --> pdb=" O   ASP K  56 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LYS L 142 " --> pdb=" O   SER L 125 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ILE L 127 " --> pdb=" O   THR L 140 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR L 140 " --> pdb=" O   ILE L 127 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LYS L 129 " --> pdb=" O   THR L 138 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   THR L 138 " --> pdb=" O   LYS L 129 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER L  81 " --> pdb=" O   LEU L  45 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   LEU L  45 " --> pdb=" O   SER L  81 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   THR L  83 " --> pdb=" O   LYS L  43 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'L' and resid 54 through 56

    526 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.83

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2515
        1.31 -     1.44: 3915
        1.44 -     1.56: 8018
        1.56 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 14520
  Sorted by residual:
  bond pdb=" CA  GLY I 103 "
       pdb=" C   GLY I 103 "
    ideal  model  delta    sigma   weight residual
    1.519  1.461  0.057 9.70e-03 1.06e+04 3.50e+01
  bond pdb=" CA  GLY C 103 "
       pdb=" C   GLY C 103 "
    ideal  model  delta    sigma   weight residual
    1.519  1.462  0.057 9.70e-03 1.06e+04 3.45e+01
  bond pdb=" CA  GLU C 102 "
       pdb=" C   GLU C 102 "
    ideal  model  delta    sigma   weight residual
    1.525  1.454  0.071 1.29e-02 6.01e+03 3.01e+01
  bond pdb=" CA  GLU I 102 "
       pdb=" C   GLU I 102 "
    ideal  model  delta    sigma   weight residual
    1.525  1.454  0.071 1.29e-02 6.01e+03 3.00e+01
  bond pdb=" CA  GLN G  91 "
       pdb=" C   GLN G  91 "
    ideal  model  delta    sigma   weight residual
    1.523  1.465  0.058 1.35e-02 5.49e+03 1.86e+01
  ... (remaining 14515 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 19225
        1.98 -     3.96: 487
        3.96 -     5.93: 49
        5.93 -     7.91: 29
        7.91 -     9.89: 10
  Bond angle restraints: 19800
  Sorted by residual:
  angle pdb=" N   ASP F  61 "
        pdb=" CA  ASP F  61 "
        pdb=" C   ASP F  61 "
      ideal   model   delta    sigma   weight residual
     111.28  116.79   -5.51 1.09e+00 8.42e-01 2.56e+01
  angle pdb=" N   ASP L  61 "
        pdb=" CA  ASP L  61 "
        pdb=" C   ASP L  61 "
      ideal   model   delta    sigma   weight residual
     111.28  116.78   -5.50 1.09e+00 8.42e-01 2.55e+01
  angle pdb=" N   ASP I  61 "
        pdb=" CA  ASP I  61 "
        pdb=" C   ASP I  61 "
      ideal   model   delta    sigma   weight residual
     111.28  116.75   -5.47 1.09e+00 8.42e-01 2.52e+01
  angle pdb=" N   ASP C  61 "
        pdb=" CA  ASP C  61 "
        pdb=" C   ASP C  61 "
      ideal   model   delta    sigma   weight residual
     111.28  116.74   -5.46 1.09e+00 8.42e-01 2.51e+01
  angle pdb=" N   ASP C  62 "
        pdb=" CA  ASP C  62 "
        pdb=" C   ASP C  62 "
      ideal   model   delta    sigma   weight residual
     110.24  117.04   -6.80 1.41e+00 5.03e-01 2.32e+01
  ... (remaining 19795 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 7886
       17.75 -    35.51: 532
       35.51 -    53.26: 74
       53.26 -    71.01: 14
       71.01 -    88.77: 14
  Dihedral angle restraints: 8520
    sinusoidal: 3288
      harmonic: 5232
  Sorted by residual:
  dihedral pdb=" C   GLU I 102 "
           pdb=" N   GLU I 102 "
           pdb=" CA  GLU I 102 "
           pdb=" CB  GLU I 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.62   -9.98     0      2.50e+00 1.60e-01 1.59e+01
  dihedral pdb=" C   GLU C 102 "
           pdb=" N   GLU C 102 "
           pdb=" CA  GLU C 102 "
           pdb=" CB  GLU C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.62   -9.98     0      2.50e+00 1.60e-01 1.59e+01
  dihedral pdb=" C   ARG E 139 "
           pdb=" N   ARG E 139 "
           pdb=" CA  ARG E 139 "
           pdb=" CB  ARG E 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.61   -8.99     0      2.50e+00 1.60e-01 1.29e+01
  ... (remaining 8517 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1900
       0.087 -    0.175: 228
       0.175 -    0.262: 14
       0.262 -    0.349: 0
       0.349 -    0.436: 6
  Chirality restraints: 2148
  Sorted by residual:
  chirality pdb=" CA  ASP F  62 "
            pdb=" N   ASP F  62 "
            pdb=" C   ASP F  62 "
            pdb=" CB  ASP F  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.76e+00
  chirality pdb=" CA  ASP I  62 "
            pdb=" N   ASP I  62 "
            pdb=" C   ASP I  62 "
            pdb=" CB  ASP I  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.76e+00
  chirality pdb=" CA  ASP C  62 "
            pdb=" N   ASP C  62 "
            pdb=" C   ASP C  62 "
            pdb=" CB  ASP C  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.76e+00
  ... (remaining 2145 not shown)

  Planarity restraints: 2580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU G  90 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.04e+00
        pdb=" C   GLU G  90 "    0.052 2.00e-02 2.50e+03
        pdb=" O   GLU G  90 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLN G  91 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  90 "   -0.015 2.00e-02 2.50e+03   3.00e-02 8.99e+00
        pdb=" C   GLU A  90 "    0.052 2.00e-02 2.50e+03
        pdb=" O   GLU A  90 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLN A  91 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  31 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   LEU A  31 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A  31 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER A  32 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2577 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 3173
        2.78 -     3.31: 11954
        3.31 -     3.84: 20948
        3.84 -     4.37: 24600
        4.37 -     4.90: 46736
  Nonbonded interactions: 107411
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F 108 "
            pdb=" OD1 ASN F 145 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR L 108 "
            pdb=" OD1 ASN L 145 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR I 108 "
            pdb=" OD1 ASN I 145 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OH  TYR C 108 "
            pdb=" OD1 ASN C 145 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP D  44 "
            pdb=" N   LEU D  45 "
     model   vdw
     2.266 3.120
  ... (remaining 107406 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     32.170
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
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      :  0.008   0.071  14520  Z= 0.436
  Angle     :  0.812   9.889  19800  Z= 0.463
  Chirality :  0.057   0.436   2148
  Planarity :  0.004   0.030   2580
  Dihedral  : 12.359  88.766   5184
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  0.80 %
    Favored  : 98.40 %
  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: -0.90 (0.17), residues: 1824
  helix:  1.22 (0.47), residues: 144
  sheet: -0.16 (0.17), residues: 864
  loop : -1.37 (0.15), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP I  18 
 PHE   0.017   0.002   PHE B 120 
 TYR   0.012   0.002   TYR K  20 
 ARG   0.004   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20235 (  462)
  hydrogen bonds       : angle       9.68250 ( 1416)
  covalent geometry    : bond        0.00830 (14520)
  covalent geometry    : angle       0.81227 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 370
  time to evaluate  : 1.473 
Fit side-chains
REVERT: A   61 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8414 (m-30)
REVERT: A  134 LYS cc_start: 0.9186 (mtpt) cc_final: 0.8831 (mtmt)
REVERT: B   27 TYR cc_start: 0.8889 (m-10) cc_final: 0.8634 (m-80)
REVERT: C   11 LYS cc_start: 0.9427 (mttp) cc_final: 0.9182 (mttm)
REVERT: C   41 LYS cc_start: 0.9401 (mttm) cc_final: 0.9165 (mttt)
REVERT: C   43 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8300 (mtpp)
REVERT: C   61 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8135 (m-30)
REVERT: C   87 MET cc_start: 0.9238 (mtp) cc_final: 0.8941 (mtp)
REVERT: C  114 ASN cc_start: 0.8767 (t0) cc_final: 0.8554 (t0)
REVERT: C  134 LYS cc_start: 0.9273 (mtmt) cc_final: 0.9069 (mtmt)
REVERT: D   44 ASP cc_start: 0.7826 (t0) cc_final: 0.7590 (t70)
REVERT: D  118 ASP cc_start: 0.7839 (t0) cc_final: 0.7493 (t0)
REVERT: E   11 LYS cc_start: 0.9337 (mttp) cc_final: 0.9106 (mttm)
REVERT: F   61 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7669 (m-30)
REVERT: F   87 MET cc_start: 0.9037 (mtp) cc_final: 0.8756 (mtp)
REVERT: G   27 TYR cc_start: 0.8997 (m-10) cc_final: 0.8748 (m-10)
REVERT: G   53 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7447 (mp0)
REVERT: G  101 ASN cc_start: 0.8676 (m-40) cc_final: 0.8451 (m-40)
REVERT: I   43 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8341 (mptt)
REVERT: K   43 LYS cc_start: 0.9091 (mtpp) cc_final: 0.7670 (mmtt)
REVERT: L   43 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8104 (mptt)
REVERT: L  121 ARG cc_start: 0.8551 (mtp-110) cc_final: 0.8162 (ttm-80)
  outliers start: 12
  outliers final: 0
  residues processed: 372
  average time/residue: 0.3163
  time to fit residues: 161.6582
Evaluate side-chains
  218 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 215
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain F residue   61 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 151 optimal weight:    4.9990
   chunk 136 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 141 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   chunk 163 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
G 101 ASN
J 101 ASN
K  29 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.088570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.074064 restraints weight = 20484.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.2647 rms_B_bonded: 1.59
r_work: 0.2540 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2410 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  14520  Z= 0.190
  Angle     :  0.576   5.142  19800  Z= 0.307
  Chirality :  0.047   0.151   2148
  Planarity :  0.004   0.029   2580
  Dihedral  :  5.163  56.417   1986
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.40 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.85 (0.17), residues: 1824
  helix:  1.46 (0.44), residues: 144
  sheet: -0.48 (0.15), residues: 936
  loop : -0.92 (0.15), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  36 
 PHE   0.015   0.002   PHE E 120 
 TYR   0.014   0.002   TYR C 108 
 ARG   0.005   0.001   ARG I 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (  462)
  hydrogen bonds       : angle       6.44709 ( 1416)
  covalent geometry    : bond        0.00461 (14520)
  covalent geometry    : angle       0.57556 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 246
  time to evaluate  : 1.434 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.9312 (mtpt) cc_final: 0.9054 (mtmt)
REVERT: B   61 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8211 (m-30)
REVERT: B   63 GLU cc_start: 0.8315 (pm20) cc_final: 0.8082 (tp30)
REVERT: C   11 LYS cc_start: 0.9469 (mttp) cc_final: 0.9261 (mttt)
REVERT: C   43 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8225 (mtpp)
REVERT: C   44 ASP cc_start: 0.8172 (m-30) cc_final: 0.7508 (m-30)
REVERT: C   61 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8408 (m-30)
REVERT: C   87 MET cc_start: 0.9313 (mtp) cc_final: 0.9090 (mtp)
REVERT: C  114 ASN cc_start: 0.8941 (t0) cc_final: 0.8723 (t0)
REVERT: D   58 SER cc_start: 0.8461 (m) cc_final: 0.8145 (p)
REVERT: F    5 ASN cc_start: 0.8618 (t0) cc_final: 0.8323 (t0)
REVERT: F   61 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.7943 (m-30)
REVERT: F   87 MET cc_start: 0.9282 (mtp) cc_final: 0.9066 (mtp)
REVERT: G   53 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8151 (mp0)
REVERT: G  101 ASN cc_start: 0.8858 (m110) cc_final: 0.8647 (m-40)
REVERT: G  102 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: G  118 ASP cc_start: 0.7802 (t0) cc_final: 0.7566 (t0)
REVERT: H  135 GLU cc_start: 0.8662 (mp0) cc_final: 0.8404 (mp0)
REVERT: I   20 TYR cc_start: 0.9085 (t80) cc_final: 0.8763 (t80)
REVERT: I   32 SER cc_start: 0.8967 (t) cc_final: 0.8645 (m)
REVERT: I   38 ARG cc_start: 0.9145 (ttt180) cc_final: 0.8906 (ttt180)
REVERT: I   43 LYS cc_start: 0.9219 (mtpt) cc_final: 0.7749 (mptt)
REVERT: I   97 LEU cc_start: 0.8965 (mt) cc_final: 0.8686 (mt)
REVERT: J  135 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8462 (mp0)
REVERT: K    5 ASN cc_start: 0.8999 (t0) cc_final: 0.8688 (t0)
REVERT: K   38 ARG cc_start: 0.9155 (ttt180) cc_final: 0.8871 (ttt90)
REVERT: L   29 ASN cc_start: 0.9370 (t0) cc_final: 0.9147 (t0)
REVERT: L  101 ASN cc_start: 0.8943 (m-40) cc_final: 0.8411 (m-40)
  outliers start: 30
  outliers final: 23
  residues processed: 270
  average time/residue: 0.2933
  time to fit residues: 110.6981
Evaluate side-chains
  213 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain E residue   37 SER
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain E residue   83 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain J residue   37 SER
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 135 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0070
   chunk 54 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 178 optimal weight:    8.9990
   overall best weight:    3.2004

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.085947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.071317 restraints weight = 20877.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.2602 rms_B_bonded: 1.62
r_work: 0.2494 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2363 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14520  Z= 0.206
  Angle     :  0.561   5.259  19800  Z= 0.299
  Chirality :  0.047   0.157   2148
  Planarity :  0.004   0.034   2580
  Dihedral  :  5.115  55.297   1984
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 10.47 %
    Favored  : 85.67 %
  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: -0.82 (0.17), residues: 1824
  helix:  1.55 (0.43), residues: 144
  sheet: -0.48 (0.15), residues: 936
  loop : -0.90 (0.16), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  36 
 PHE   0.014   0.002   PHE E 120 
 TYR   0.011   0.002   TYR C 108 
 ARG   0.003   0.001   ARG I 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  462)
  hydrogen bonds       : angle       5.97678 ( 1416)
  covalent geometry    : bond        0.00507 (14520)
  covalent geometry    : angle       0.56135 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 196
  time to evaluate  : 1.571 
Fit side-chains
REVERT: A   61 ASP cc_start: 0.8795 (t0) cc_final: 0.8577 (t0)
REVERT: A  134 LYS cc_start: 0.9319 (mtpt) cc_final: 0.9048 (mtmt)
REVERT: B   61 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8179 (m-30)
REVERT: C   11 LYS cc_start: 0.9483 (mttp) cc_final: 0.9265 (mttt)
REVERT: C   43 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8330 (mtpp)
REVERT: C   44 ASP cc_start: 0.8286 (m-30) cc_final: 0.7607 (m-30)
REVERT: C   87 MET cc_start: 0.9484 (mtp) cc_final: 0.9238 (mtp)
REVERT: G    5 ASN cc_start: 0.9043 (t0) cc_final: 0.8798 (t0)
REVERT: G   53 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8207 (mp0)
REVERT: H  135 GLU cc_start: 0.8684 (mp0) cc_final: 0.8367 (mp0)
REVERT: I   20 TYR cc_start: 0.9071 (t80) cc_final: 0.8726 (t80)
REVERT: I   32 SER cc_start: 0.8999 (t) cc_final: 0.8657 (m)
REVERT: I   43 LYS cc_start: 0.9108 (mtpt) cc_final: 0.7575 (mptt)
REVERT: J  101 ASN cc_start: 0.8810 (m-40) cc_final: 0.8577 (m110)
REVERT: K    5 ASN cc_start: 0.8777 (t0) cc_final: 0.8494 (t0)
REVERT: K  102 GLU cc_start: 0.8096 (tt0) cc_final: 0.7436 (mt-10)
REVERT: K  118 ASP cc_start: 0.8202 (t0) cc_final: 0.7818 (t0)
REVERT: K  135 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8108 (mp0)
REVERT: L   29 ASN cc_start: 0.9235 (t0) cc_final: 0.8994 (t0)
REVERT: L  101 ASN cc_start: 0.8938 (m-40) cc_final: 0.8434 (m-40)
  outliers start: 58
  outliers final: 49
  residues processed: 249
  average time/residue: 0.2847
  time to fit residues: 99.8463
Evaluate side-chains
  236 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 186
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   37 SER
Chi-restraints excluded: chain E residue   83 THR
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain J residue   37 SER
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue   84 LEU
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 158 optimal weight:   10.0000
   chunk 96 optimal weight:    8.9990
   chunk 139 optimal weight:    0.0270
   chunk 113 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 132 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    2.4044

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.086977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.072360 restraints weight = 20556.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.2617 rms_B_bonded: 1.60
r_work: 0.2511 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2381 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  14520  Z= 0.159
  Angle     :  0.520   5.177  19800  Z= 0.275
  Chirality :  0.045   0.155   2148
  Planarity :  0.003   0.033   2580
  Dihedral  :  4.519  16.089   1980
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 11.87 %
    Favored  : 83.67 %
  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: -0.77 (0.17), residues: 1824
  helix:  1.57 (0.42), residues: 144
  sheet: -0.45 (0.16), residues: 936
  loop : -0.85 (0.16), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  36 
 PHE   0.013   0.002   PHE E 120 
 TYR   0.010   0.001   TYR E 108 
 ARG   0.004   0.000   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 (  462)
  hydrogen bonds       : angle       5.59247 ( 1416)
  covalent geometry    : bond        0.00388 (14520)
  covalent geometry    : angle       0.52037 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 196
  time to evaluate  : 1.569 
Fit side-chains
REVERT: A   61 ASP cc_start: 0.8691 (t0) cc_final: 0.8477 (t0)
REVERT: A  134 LYS cc_start: 0.9291 (mtpt) cc_final: 0.8984 (mtmt)
REVERT: B   61 ASP cc_start: 0.8682 (m-30) cc_final: 0.8323 (m-30)
REVERT: C   11 LYS cc_start: 0.9456 (mttp) cc_final: 0.9251 (mttt)
REVERT: C   43 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8464 (mtpp)
REVERT: C   44 ASP cc_start: 0.8259 (m-30) cc_final: 0.8032 (m-30)
REVERT: F    8 MET cc_start: 0.9058 (mmm) cc_final: 0.8390 (mtm)
REVERT: F   10 VAL cc_start: 0.9336 (p) cc_final: 0.8965 (m)
REVERT: G   53 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8163 (mp0)
REVERT: H  135 GLU cc_start: 0.8685 (mp0) cc_final: 0.8391 (mp0)
REVERT: I   20 TYR cc_start: 0.9032 (t80) cc_final: 0.8483 (t80)
REVERT: I   32 SER cc_start: 0.9005 (t) cc_final: 0.8650 (m)
REVERT: I   43 LYS cc_start: 0.9078 (mtpt) cc_final: 0.7643 (mptt)
REVERT: J  101 ASN cc_start: 0.8824 (m-40) cc_final: 0.8561 (m110)
REVERT: K    5 ASN cc_start: 0.8710 (t0) cc_final: 0.8340 (t0)
REVERT: K   74 GLN cc_start: 0.9063 (tt0) cc_final: 0.8745 (tt0)
REVERT: K  135 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8054 (mp0)
REVERT: L   29 ASN cc_start: 0.9262 (t0) cc_final: 0.8954 (t0)
REVERT: L  101 ASN cc_start: 0.8929 (m-40) cc_final: 0.8413 (m-40)
  outliers start: 67
  outliers final: 55
  residues processed: 255
  average time/residue: 0.2844
  time to fit residues: 102.2096
Evaluate side-chains
  240 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 185
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain E residue   83 THR
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain G residue  124 VAL
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 155 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0470
   overall best weight:    1.8086

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.087963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.073316 restraints weight = 20697.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2638 rms_B_bonded: 1.62
r_work: 0.2532 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2402 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14520  Z= 0.128
  Angle     :  0.498   6.094  19800  Z= 0.260
  Chirality :  0.044   0.155   2148
  Planarity :  0.003   0.032   2580
  Dihedral  :  4.273  15.906   1980
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 12.33 %
    Favored  : 83.07 %
  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: -0.63 (0.17), residues: 1824
  helix:  1.72 (0.41), residues: 144
  sheet: -0.37 (0.16), residues: 936
  loop : -0.74 (0.17), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  36 
 PHE   0.010   0.001   PHE E 120 
 TYR   0.009   0.001   TYR B 108 
 ARG   0.005   0.000   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02951 (  462)
  hydrogen bonds       : angle       5.21005 ( 1416)
  covalent geometry    : bond        0.00309 (14520)
  covalent geometry    : angle       0.49773 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 194
  time to evaluate  : 1.402 
Fit side-chains
REVERT: A   10 VAL cc_start: 0.9232 (p) cc_final: 0.8872 (m)
REVERT: A   61 ASP cc_start: 0.8531 (t0) cc_final: 0.8286 (t0)
REVERT: A  134 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8981 (mtmt)
REVERT: B   61 ASP cc_start: 0.8617 (m-30) cc_final: 0.8153 (m-30)
REVERT: B   87 MET cc_start: 0.9346 (mtm) cc_final: 0.9130 (mtp)
REVERT: B  118 ASP cc_start: 0.8868 (m-30) cc_final: 0.8515 (m-30)
REVERT: C   10 VAL cc_start: 0.9413 (p) cc_final: 0.9100 (m)
REVERT: C   11 LYS cc_start: 0.9436 (mttp) cc_final: 0.9209 (mttt)
REVERT: C   43 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8177 (mtpp)
REVERT: F    8 MET cc_start: 0.8992 (mmm) cc_final: 0.8339 (mtm)
REVERT: F   10 VAL cc_start: 0.9301 (p) cc_final: 0.8970 (m)
REVERT: F  114 ASN cc_start: 0.8958 (t0) cc_final: 0.8737 (t0)
REVERT: G   53 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8189 (mp0)
REVERT: G   97 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8725 (mt)
REVERT: H   42 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8765 (t)
REVERT: H  135 GLU cc_start: 0.8589 (mp0) cc_final: 0.8248 (mp0)
REVERT: I   32 SER cc_start: 0.9012 (t) cc_final: 0.8662 (m)
REVERT: I   43 LYS cc_start: 0.9048 (mtpt) cc_final: 0.7596 (mptt)
REVERT: J  101 ASN cc_start: 0.8872 (m-40) cc_final: 0.8592 (m110)
REVERT: K    5 ASN cc_start: 0.8651 (t0) cc_final: 0.8247 (t0)
REVERT: K   74 GLN cc_start: 0.9088 (tt0) cc_final: 0.8725 (tt0)
REVERT: K  118 ASP cc_start: 0.8040 (t0) cc_final: 0.7647 (t0)
REVERT: L   29 ASN cc_start: 0.9277 (t0) cc_final: 0.8915 (t0)
REVERT: L   87 MET cc_start: 0.8894 (mtm) cc_final: 0.8664 (mtt)
REVERT: L  101 ASN cc_start: 0.8914 (m-40) cc_final: 0.8521 (m-40)
REVERT: L  153 GLU cc_start: 0.8830 (pm20) cc_final: 0.8042 (pm20)
  outliers start: 69
  outliers final: 61
  residues processed: 256
  average time/residue: 0.2735
  time to fit residues: 99.1930
Evaluate side-chains
  252 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 189
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain E residue   83 THR
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain G residue   97 LEU
Chi-restraints excluded: chain G residue  124 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain I residue   97 LEU
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue   84 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 153 optimal weight:    0.0980
   chunk 168 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 93 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 174 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    4.8186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.084189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.069327 restraints weight = 21240.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.2562 rms_B_bonded: 1.65
r_work: 0.2452 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2321 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  14520  Z= 0.295
  Angle     :  0.625   7.077  19800  Z= 0.330
  Chirality :  0.049   0.167   2148
  Planarity :  0.004   0.038   2580
  Dihedral  :  5.023  17.525   1980
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 12.87 %
    Favored  : 81.40 %
  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: -0.92 (0.17), residues: 1824
  helix:  1.44 (0.43), residues: 144
  sheet: -0.52 (0.16), residues: 936
  loop : -0.98 (0.17), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E  36 
 PHE   0.020   0.002   PHE C 120 
 TYR   0.011   0.002   TYR E 108 
 ARG   0.004   0.001   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  462)
  hydrogen bonds       : angle       5.66891 ( 1416)
  covalent geometry    : bond        0.00730 (14520)
  covalent geometry    : angle       0.62474 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 181
  time to evaluate  : 1.521 
Fit side-chains
REVERT: A   61 ASP cc_start: 0.8674 (t0) cc_final: 0.8456 (t0)
REVERT: A  134 LYS cc_start: 0.9327 (mtpt) cc_final: 0.9111 (mtmt)
REVERT: B   61 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8170 (m-30)
REVERT: B  118 ASP cc_start: 0.8855 (m-30) cc_final: 0.8586 (m-30)
REVERT: F    8 MET cc_start: 0.8993 (mmm) cc_final: 0.8384 (mtm)
REVERT: F  114 ASN cc_start: 0.9017 (t0) cc_final: 0.8737 (t0)
REVERT: G   53 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8264 (mp0)
REVERT: I    8 MET cc_start: 0.8696 (mmm) cc_final: 0.8472 (mmm)
REVERT: I   32 SER cc_start: 0.9047 (t) cc_final: 0.8691 (m)
REVERT: I   43 LYS cc_start: 0.9132 (mtpt) cc_final: 0.7820 (mptt)
REVERT: K    5 ASN cc_start: 0.8874 (t0) cc_final: 0.8409 (t0)
REVERT: L   29 ASN cc_start: 0.9343 (t0) cc_final: 0.8974 (t0)
REVERT: L  101 ASN cc_start: 0.8958 (m-40) cc_final: 0.8534 (m-40)
REVERT: L  153 GLU cc_start: 0.9008 (pm20) cc_final: 0.8702 (pm20)
  outliers start: 86
  outliers final: 70
  residues processed: 256
  average time/residue: 0.2819
  time to fit residues: 102.5196
Evaluate side-chains
  249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 178
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   46 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   97 LEU
Chi-restraints excluded: chain J residue   37 SER
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain K residue  146 VAL
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue   84 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 122 optimal weight:    0.1980
   chunk 67 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 36 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 171 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 162 optimal weight:    7.9990
   chunk 163 optimal weight:    5.9990
   overall best weight:    1.6984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.087109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.072536 restraints weight = 20844.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.2626 rms_B_bonded: 1.61
r_work: 0.2521 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2390 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14520  Z= 0.124
  Angle     :  0.504   6.092  19800  Z= 0.263
  Chirality :  0.044   0.156   2148
  Planarity :  0.003   0.034   2580
  Dihedral  :  4.370  16.868   1980
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 13.93 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.75 (0.17), residues: 1824
  helix:  1.62 (0.42), residues: 144
  sheet: -0.44 (0.16), residues: 936
  loop : -0.84 (0.17), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  36 
 PHE   0.010   0.001   PHE E 120 
 TYR   0.009   0.001   TYR B 108 
 ARG   0.005   0.000   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02976 (  462)
  hydrogen bonds       : angle       5.18535 ( 1416)
  covalent geometry    : bond        0.00300 (14520)
  covalent geometry    : angle       0.50388 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 184
  time to evaluate  : 1.465 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.9283 (mtpt) cc_final: 0.9012 (mtmt)
REVERT: B   61 ASP cc_start: 0.8501 (m-30) cc_final: 0.8148 (m-30)
REVERT: F    8 MET cc_start: 0.8967 (mmm) cc_final: 0.8327 (mtm)
REVERT: F   10 VAL cc_start: 0.9318 (p) cc_final: 0.9006 (m)
REVERT: G   53 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8159 (mp0)
REVERT: H  135 GLU cc_start: 0.8624 (mp0) cc_final: 0.8246 (mp0)
REVERT: I   20 TYR cc_start: 0.8963 (t80) cc_final: 0.8553 (t80)
REVERT: I   32 SER cc_start: 0.9014 (t) cc_final: 0.8657 (m)
REVERT: I   43 LYS cc_start: 0.9094 (mtpt) cc_final: 0.7728 (mptt)
REVERT: J  101 ASN cc_start: 0.8864 (m-40) cc_final: 0.8563 (m110)
REVERT: K    5 ASN cc_start: 0.8723 (t0) cc_final: 0.8237 (t0)
REVERT: K   42 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8668 (p)
REVERT: K  118 ASP cc_start: 0.8104 (t0) cc_final: 0.7714 (t0)
REVERT: K  135 GLU cc_start: 0.8401 (mp0) cc_final: 0.8135 (mp0)
REVERT: L   87 MET cc_start: 0.8952 (mtm) cc_final: 0.8712 (mtt)
REVERT: L  101 ASN cc_start: 0.8895 (m-40) cc_final: 0.8396 (m-40)
  outliers start: 69
  outliers final: 63
  residues processed: 243
  average time/residue: 0.2641
  time to fit residues: 91.5154
Evaluate side-chains
  242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 178
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue  124 VAL
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain I residue   97 LEU
Chi-restraints excluded: chain I residue  125 SER
Chi-restraints excluded: chain J residue   37 SER
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   37 SER
Chi-restraints excluded: chain K residue   42 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain K residue  132 THR
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue   84 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 108 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 126 optimal weight:    7.9990
   chunk 142 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 121 optimal weight:    5.9990
   chunk 141 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    3.2786

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

Flipped N/Q/H residues before XYZ refinement:
D 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.084929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.070369 restraints weight = 21011.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.2587 rms_B_bonded: 1.62
r_work: 0.2480 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2349 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14520  Z= 0.208
  Angle     :  0.562   6.997  19800  Z= 0.295
  Chirality :  0.046   0.163   2148
  Planarity :  0.004   0.035   2580
  Dihedral  :  4.657  17.429   1980
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 13.67 %
    Favored  : 81.07 %
  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: -0.81 (0.17), residues: 1824
  helix:  1.52 (0.42), residues: 144
  sheet: -0.44 (0.16), residues: 936
  loop : -0.92 (0.17), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  36 
 PHE   0.015   0.002   PHE C 120 
 TYR   0.010   0.002   TYR C 108 
 ARG   0.005   0.000   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03362 (  462)
  hydrogen bonds       : angle       5.35082 ( 1416)
  covalent geometry    : bond        0.00513 (14520)
  covalent geometry    : angle       0.56228 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 179
  time to evaluate  : 1.459 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.9301 (mtpt) cc_final: 0.9100 (mtmt)
REVERT: C   63 GLU cc_start: 0.8143 (pm20) cc_final: 0.7865 (pm20)
REVERT: F    8 MET cc_start: 0.9005 (mmm) cc_final: 0.8382 (mtm)
REVERT: F   10 VAL cc_start: 0.9339 (p) cc_final: 0.8993 (m)
REVERT: G   53 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8211 (mp0)
REVERT: I   20 TYR cc_start: 0.8960 (t80) cc_final: 0.8599 (t80)
REVERT: I   32 SER cc_start: 0.9033 (t) cc_final: 0.8669 (m)
REVERT: I   43 LYS cc_start: 0.9109 (mtpt) cc_final: 0.7774 (mptt)
REVERT: I  118 ASP cc_start: 0.8123 (m-30) cc_final: 0.7802 (m-30)
REVERT: J  101 ASN cc_start: 0.8892 (m-40) cc_final: 0.8554 (m110)
REVERT: K    5 ASN cc_start: 0.8804 (t0) cc_final: 0.8293 (t0)
REVERT: K   42 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8532 (p)
REVERT: K  135 GLU cc_start: 0.8391 (mp0) cc_final: 0.7953 (mp0)
REVERT: L   29 ASN cc_start: 0.9193 (t0) cc_final: 0.8942 (t0)
REVERT: L  101 ASN cc_start: 0.8938 (m-40) cc_final: 0.8427 (m-40)
  outliers start: 79
  outliers final: 72
  residues processed: 245
  average time/residue: 0.2743
  time to fit residues: 95.8917
Evaluate side-chains
  252 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 179
  time to evaluate  : 1.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   46 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue  124 VAL
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   97 LEU
Chi-restraints excluded: chain I residue  125 SER
Chi-restraints excluded: chain J residue   37 SER
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   42 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain K residue  132 THR
Chi-restraints excluded: chain K residue  146 VAL
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue   84 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 148 optimal weight:    6.9990
   chunk 167 optimal weight:    0.6980
   chunk 114 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 129 optimal weight:    5.9990
   overall best weight:    2.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.086401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.071810 restraints weight = 20716.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2613 rms_B_bonded: 1.62
r_work: 0.2506 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2375 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14520  Z= 0.155
  Angle     :  0.521   7.273  19800  Z= 0.272
  Chirality :  0.045   0.158   2148
  Planarity :  0.004   0.035   2580
  Dihedral  :  4.415  17.186   1980
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 14.53 %
    Favored  : 80.93 %
  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: -0.75 (0.17), residues: 1824
  helix:  1.61 (0.42), residues: 144
  sheet: -0.41 (0.16), residues: 936
  loop : -0.87 (0.17), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  36 
 PHE   0.012   0.001   PHE E 120 
 TYR   0.010   0.001   TYR E 108 
 ARG   0.005   0.000   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03067 (  462)
  hydrogen bonds       : angle       5.18438 ( 1416)
  covalent geometry    : bond        0.00378 (14520)
  covalent geometry    : angle       0.52133 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 183
  time to evaluate  : 1.461 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.9292 (mtpt) cc_final: 0.9053 (mtmt)
REVERT: B   61 ASP cc_start: 0.8474 (m-30) cc_final: 0.8122 (m-30)
REVERT: C   63 GLU cc_start: 0.8179 (pm20) cc_final: 0.7929 (pm20)
REVERT: F    8 MET cc_start: 0.8989 (mmm) cc_final: 0.8365 (mtm)
REVERT: F   10 VAL cc_start: 0.9315 (p) cc_final: 0.8992 (m)
REVERT: G   53 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8180 (mp0)
REVERT: I   20 TYR cc_start: 0.8958 (t80) cc_final: 0.8568 (t80)
REVERT: I   32 SER cc_start: 0.9039 (t) cc_final: 0.8591 (m)
REVERT: I   43 LYS cc_start: 0.9093 (mtpt) cc_final: 0.7741 (mptt)
REVERT: J  101 ASN cc_start: 0.8904 (m-40) cc_final: 0.8595 (m110)
REVERT: K    5 ASN cc_start: 0.8750 (t0) cc_final: 0.8231 (t0)
REVERT: K   42 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8529 (p)
REVERT: L   29 ASN cc_start: 0.9200 (t0) cc_final: 0.8924 (t0)
REVERT: L  101 ASN cc_start: 0.8922 (m-40) cc_final: 0.8425 (m-40)
  outliers start: 68
  outliers final: 66
  residues processed: 238
  average time/residue: 0.3053
  time to fit residues: 102.8499
Evaluate side-chains
  249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 182
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   46 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue  124 VAL
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   97 LEU
Chi-restraints excluded: chain I residue  125 SER
Chi-restraints excluded: chain J residue   37 SER
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   42 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain K residue  132 THR
Chi-restraints excluded: chain K residue  146 VAL
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue   84 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 178 optimal weight:    8.9990
   chunk 158 optimal weight:    3.9990
   chunk 142 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 173 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 141 optimal weight:   10.0000
   overall best weight:    2.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.086415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.071876 restraints weight = 20862.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.2616 rms_B_bonded: 1.61
r_work: 0.2510 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2380 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  14520  Z= 0.149
  Angle     :  0.518   7.174  19800  Z= 0.271
  Chirality :  0.045   0.158   2148
  Planarity :  0.004   0.034   2580
  Dihedral  :  4.375  17.060   1980
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 14.20 %
    Favored  : 80.93 %
  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: -0.72 (0.17), residues: 1824
  helix:  1.69 (0.42), residues: 144
  sheet: -0.40 (0.16), residues: 936
  loop : -0.86 (0.17), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  36 
 PHE   0.012   0.001   PHE E 120 
 TYR   0.009   0.001   TYR C 108 
 ARG   0.006   0.000   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  462)
  hydrogen bonds       : angle       5.15320 ( 1416)
  covalent geometry    : bond        0.00363 (14520)
  covalent geometry    : angle       0.51812 (19800)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 183
  time to evaluate  : 1.560 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.9283 (mtpt) cc_final: 0.9057 (mtmt)
REVERT: B   61 ASP cc_start: 0.8441 (m-30) cc_final: 0.7987 (m-30)
REVERT: C   63 GLU cc_start: 0.8248 (pm20) cc_final: 0.7993 (pm20)
REVERT: F    8 MET cc_start: 0.8968 (mmm) cc_final: 0.8384 (mtm)
REVERT: F   10 VAL cc_start: 0.9295 (p) cc_final: 0.8974 (m)
REVERT: G   53 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8169 (mp0)
REVERT: I   20 TYR cc_start: 0.8956 (t80) cc_final: 0.8572 (t80)
REVERT: I   32 SER cc_start: 0.9113 (t) cc_final: 0.8630 (m)
REVERT: I   43 LYS cc_start: 0.9071 (mtpt) cc_final: 0.7727 (mptt)
REVERT: J  101 ASN cc_start: 0.8908 (m-40) cc_final: 0.8599 (m110)
REVERT: K    5 ASN cc_start: 0.8725 (t0) cc_final: 0.8191 (t0)
REVERT: K   42 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8526 (p)
REVERT: K  118 ASP cc_start: 0.8108 (t0) cc_final: 0.7737 (t0)
REVERT: K  135 GLU cc_start: 0.8247 (mp0) cc_final: 0.7862 (mp0)
REVERT: L   29 ASN cc_start: 0.9204 (t0) cc_final: 0.8917 (t0)
REVERT: L  101 ASN cc_start: 0.8919 (m-40) cc_final: 0.8422 (m-40)
  outliers start: 73
  outliers final: 70
  residues processed: 245
  average time/residue: 0.2731
  time to fit residues: 95.5738
Evaluate side-chains
  251 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 180
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   54 SER
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   54 SER
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain F residue   46 THR
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 SER
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue  124 VAL
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   37 SER
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain I residue   81 SER
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   97 LEU
Chi-restraints excluded: chain I residue  125 SER
Chi-restraints excluded: chain J residue   37 SER
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   97 LEU
Chi-restraints excluded: chain K residue    3 VAL
Chi-restraints excluded: chain K residue   42 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain K residue   91 GLN
Chi-restraints excluded: chain K residue  132 THR
Chi-restraints excluded: chain K residue  146 VAL
Chi-restraints excluded: chain L residue   37 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue   84 LEU
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  126 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 129 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 155 optimal weight:    7.9990
   chunk 100 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 97 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 160 optimal weight:    0.9990
   chunk 172 optimal weight:    9.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
D  29 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.089489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.074892 restraints weight = 20659.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2660 rms_B_bonded: 1.62
r_work: 0.2554 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2424 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14520  Z= 0.097
  Angle     :  0.477   6.512  19800  Z= 0.247
  Chirality :  0.043   0.153   2148
  Planarity :  0.003   0.038   2580
  Dihedral  :  3.985  16.103   1980
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 14.73 %
    Favored  : 80.93 %
  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: -0.54 (0.18), residues: 1824
  helix:  1.90 (0.41), residues: 144
  sheet: -0.29 (0.16), residues: 936
  loop : -0.75 (0.18), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  36 
 PHE   0.008   0.001   PHE B 120 
 TYR   0.009   0.001   TYR B 108 
 ARG   0.008   0.000   ARG F 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02678 (  462)
  hydrogen bonds       : angle       4.85286 ( 1416)
  covalent geometry    : bond        0.00233 (14520)
  covalent geometry    : angle       0.47657 (19800)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5987.18 seconds
wall clock time: 104 minutes 39.34 seconds (6279.34 seconds total)