Starting phenix.real_space_refine
on Thu May 15 18:46:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g8y_29858/05_2025/8g8y_29858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g8y_29858/05_2025/8g8y_29858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g8y_29858/05_2025/8g8y_29858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g8y_29858/05_2025/8g8y_29858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g8y_29858/05_2025/8g8y_29858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g8y_29858/05_2025/8g8y_29858.cif"
  }
  resolution = 3.8
  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=   0.004
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      72      5.16       5
     C    8919      2.51       5
     N    2243      2.21       5
     O    2483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 13717
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1144
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 11, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1136
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 11, 'TRANS': 130}
    Chain: "C"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1136
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 11, 'TRANS': 130}
    Chain: "D"
      Number of atoms: 1144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1144
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 11, 'TRANS': 131}
    Chain: "E"
      Number of atoms: 1151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1151
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 12, 'TRANS': 131}
    Chain: "F"
      Number of atoms: 1144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1144
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 11, 'TRANS': 131}
    Chain: "G"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1136
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 11, 'TRANS': 130}
    Chain: "H"
      Number of atoms: 1144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1144
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 11, 'TRANS': 131}
    Chain: "I"
      Number of atoms: 1144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1144
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 11, 'TRANS': 131}
    Chain: "J"
      Number of atoms: 1151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1151
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 12, 'TRANS': 131}
    Chain: "K"
      Number of atoms: 1151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1151
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 12, 'TRANS': 131}
    Chain: "L"
      Number of atoms: 1136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1136
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 11, 'TRANS': 130}
  Time building chain proxies: 9.53, per 1000 atoms: 0.69
  Number of scatterers: 13717
  At special positions: 0
  Unit cell: (182.82, 180.604, 75.344, 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      72     16.00
     O    2483      8.00
     N    2243      7.00
     C    8919      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: 3.13
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3286

  Finding SS restraints...
    Secondary structure from input PDB file:
      100 helices and 0 sheets defined
      81.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
      removed outlier: 3.651A  pdb=" N   GLY A  10 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 18
      removed outlier: 3.695A  pdb=" N   PHE A  18 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 24
      removed outlier: 3.813A  pdb=" N   PHE A  24 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 44
      removed outlier: 3.637A  pdb=" N   ARG A  39 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   GLU A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ALA A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 76
      removed outlier: 3.957A  pdb=" N   THR A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA A  54 " --> pdb=" O   PRO A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 92
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 4.105A  pdb=" N   PHE A  97 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 128
    Processing helix  chain 'A' and resid 129 through 133
    Processing helix  chain 'B' and resid 14 through 19
      removed outlier: 3.964A  pdb=" N   PHE B  18 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU B  19 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 24
      removed outlier: 3.933A  pdb=" N   PHE B  24 " --> pdb=" O   SER B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 38
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.854A  pdb=" N   THR B  53 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA B  54 " --> pdb=" O   PRO B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 111
      removed outlier: 4.257A  pdb=" N   MET B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLY B  94 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LYS B  96 " --> pdb=" O   ASN B  92 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE B  97 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 128
      removed outlier: 3.751A  pdb=" N   VAL B 124 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TRP B 125 " --> pdb=" O   SER B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 133
    Processing helix  chain 'C' and resid 6 through 10
    Processing helix  chain 'C' and resid 12 through 17
    Processing helix  chain 'C' and resid 20 through 24
      removed outlier: 3.896A  pdb=" N   PHE C  24 " --> pdb=" O   SER C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 44
      removed outlier: 3.530A  pdb=" N   LEU C  30 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG C  39 " --> pdb=" O   SER C  35 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLU C  40 " --> pdb=" O   ALA C  36 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ALA C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU C  43 " --> pdb=" O   ARG C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 76
      removed outlier: 3.861A  pdb=" N   THR C  53 " --> pdb=" O   SER C  49 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA C  54 " --> pdb=" O   PRO C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 111
      removed outlier: 4.109A  pdb=" N   MET C  93 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   GLY C  94 " --> pdb=" O   ASN C  90 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU C  95 " --> pdb=" O   THR C  91 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   LYS C  96 " --> pdb=" O   ASN C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 127
      removed outlier: 3.504A  pdb=" N   LEU C 119 " --> pdb=" O   VAL C 115 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL C 120 " --> pdb=" O   ILE C 116 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ARG C 127 " --> pdb=" O   GLY C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 133
    Processing helix  chain 'D' and resid 6 through 10
    Processing helix  chain 'D' and resid 15 through 19
      removed outlier: 3.961A  pdb=" N   LEU D  19 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 24
      removed outlier: 4.061A  pdb=" N   PHE D  24 " --> pdb=" O   SER D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 44
      removed outlier: 3.513A  pdb=" N   LEU D  30 " --> pdb=" O   SER D  26 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG D  39 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLU D  40 " --> pdb=" O   ALA D  36 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ALA D  41 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 3.902A  pdb=" N   THR D  53 " --> pdb=" O   SER D  49 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA D  54 " --> pdb=" O   PRO D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 111
      removed outlier: 4.012A  pdb=" N   GLY D  94 " --> pdb=" O   ASN D  90 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   LEU D  95 " --> pdb=" O   THR D  91 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   LYS D  96 " --> pdb=" O   ASN D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 128
      removed outlier: 3.640A  pdb=" N   THR D 128 " --> pdb=" O   VAL D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 133
    Processing helix  chain 'E' and resid 6 through 10
    Processing helix  chain 'E' and resid 12 through 17
    Processing helix  chain 'E' and resid 26 through 38
    Processing helix  chain 'E' and resid 39 through 44
    Processing helix  chain 'E' and resid 49 through 76
      removed outlier: 3.962A  pdb=" N   THR E  53 " --> pdb=" O   SER E  49 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA E  54 " --> pdb=" O   PRO E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 92
    Processing helix  chain 'E' and resid 93 through 111
      removed outlier: 4.016A  pdb=" N   PHE E  97 " --> pdb=" O   MET E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 128
      removed outlier: 3.589A  pdb=" N   VAL E 120 " --> pdb=" O   ILE E 116 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR E 128 " --> pdb=" O   VAL E 124 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 133
    Processing helix  chain 'F' and resid 6 through 10
      removed outlier: 3.567A  pdb=" N   GLY F  10 " --> pdb=" O   LYS F   7 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 17
    Processing helix  chain 'F' and resid 20 through 24
      removed outlier: 4.011A  pdb=" N   PHE F  24 " --> pdb=" O   SER F  21 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 26 through 43
      removed outlier: 3.698A  pdb=" N   ARG F  39 " --> pdb=" O   SER F  35 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLU F  40 " --> pdb=" O   ALA F  36 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ALA F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.816A  pdb=" N   THR F  53 " --> pdb=" O   SER F  49 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA F  54 " --> pdb=" O   PRO F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 93
    Processing helix  chain 'F' and resid 93 through 111
    Processing helix  chain 'F' and resid 111 through 128
      removed outlier: 3.536A  pdb=" N   LEU F 119 " --> pdb=" O   VAL F 115 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL F 120 " --> pdb=" O   ILE F 116 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 133
    Processing helix  chain 'G' and resid 12 through 17
    Processing helix  chain 'G' and resid 18 through 19
      No H-bonds generated for 'chain 'G' and resid 18 through 19'
    Processing helix  chain 'G' and resid 20 through 24
      removed outlier: 3.667A  pdb=" N   PHE G  24 " --> pdb=" O   SER G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 38
    Processing helix  chain 'G' and resid 49 through 76
      removed outlier: 3.795A  pdb=" N   THR G  53 " --> pdb=" O   SER G  49 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA G  54 " --> pdb=" O   PRO G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 78 through 111
      removed outlier: 4.054A  pdb=" N   MET G  93 " --> pdb=" O   VAL G  89 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLY G  94 " --> pdb=" O   ASN G  90 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   LYS G  96 " --> pdb=" O   ASN G  92 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE G  97 " --> pdb=" O   MET G  93 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 128
      removed outlier: 3.737A  pdb=" N   THR G 128 " --> pdb=" O   VAL G 124 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 129 through 133
    Processing helix  chain 'H' and resid 4 through 10
      removed outlier: 3.521A  pdb=" N   LYS H   7 " --> pdb=" O   ASP H   4 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   GLU H   8 " --> pdb=" O   PRO H   5 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY H  10 " --> pdb=" O   LYS H   7 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 14 through 18
      removed outlier: 3.560A  pdb=" N   PHE H  18 " --> pdb=" O   LEU H  15 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 20 through 24
      removed outlier: 3.760A  pdb=" N   PHE H  24 " --> pdb=" O   SER H  21 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 26 through 38
      removed outlier: 3.537A  pdb=" N   LEU H  30 " --> pdb=" O   SER H  26 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 38 through 43
      removed outlier: 3.549A  pdb=" N   LEU H  42 " --> pdb=" O   TYR H  38 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU H  43 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 38 through 43'
    Processing helix  chain 'H' and resid 49 through 76
      removed outlier: 3.963A  pdb=" N   THR H  53 " --> pdb=" O   SER H  49 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA H  54 " --> pdb=" O   PRO H  50 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 78 through 92
    Processing helix  chain 'H' and resid 93 through 111
      removed outlier: 3.869A  pdb=" N   PHE H  97 " --> pdb=" O   MET H  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 112 through 128
      removed outlier: 3.501A  pdb=" N   THR H 128 " --> pdb=" O   VAL H 124 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 129 through 133
    Processing helix  chain 'I' and resid 6 through 10
      removed outlier: 3.539A  pdb=" N   GLY I  10 " --> pdb=" O   LYS I   7 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 12 through 17
    Processing helix  chain 'I' and resid 20 through 24
      removed outlier: 3.898A  pdb=" N   PHE I  24 " --> pdb=" O   SER I  21 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 26 through 44
      removed outlier: 3.794A  pdb=" N   ARG I  39 " --> pdb=" O   SER I  35 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   GLU I  40 " --> pdb=" O   ALA I  36 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ALA I  41 " --> pdb=" O   LEU I  37 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER I  44 " --> pdb=" O   GLU I  40 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 49 through 75
      removed outlier: 3.831A  pdb=" N   THR I  53 " --> pdb=" O   SER I  49 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA I  54 " --> pdb=" O   PRO I  50 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 78 through 111
      removed outlier: 4.176A  pdb=" N   MET I  93 " --> pdb=" O   VAL I  89 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   GLY I  94 " --> pdb=" O   ASN I  90 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU I  95 " --> pdb=" O   THR I  91 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   LYS I  96 " --> pdb=" O   ASN I  92 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 111 through 127
      removed outlier: 3.510A  pdb=" N   LEU I 119 " --> pdb=" O   VAL I 115 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   VAL I 120 " --> pdb=" O   ILE I 116 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 129 through 133
    Processing helix  chain 'J' and resid 6 through 10
    Processing helix  chain 'J' and resid 14 through 18
      removed outlier: 3.693A  pdb=" N   PHE J  18 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 26 through 44
      removed outlier: 3.539A  pdb=" N   LEU J  30 " --> pdb=" O   SER J  26 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG J  39 " --> pdb=" O   SER J  35 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLU J  40 " --> pdb=" O   ALA J  36 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ALA J  41 " --> pdb=" O   LEU J  37 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER J  44 " --> pdb=" O   GLU J  40 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 49 through 76
      removed outlier: 3.940A  pdb=" N   THR J  53 " --> pdb=" O   SER J  49 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA J  54 " --> pdb=" O   PRO J  50 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 78 through 111
      removed outlier: 3.995A  pdb=" N   GLY J  94 " --> pdb=" O   ASN J  90 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   LEU J  95 " --> pdb=" O   THR J  91 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   LYS J  96 " --> pdb=" O   ASN J  92 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 111 through 128
      removed outlier: 3.629A  pdb=" N   THR J 128 " --> pdb=" O   VAL J 124 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 129 through 133
      removed outlier: 3.669A  pdb=" N   TYR J 132 " --> pdb=" O   PRO J 129 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG J 133 " --> pdb=" O   PRO J 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 129 through 133'
    Processing helix  chain 'K' and resid 6 through 10
    Processing helix  chain 'K' and resid 14 through 19
      removed outlier: 3.669A  pdb=" N   PHE K  18 " --> pdb=" O   LEU K  15 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU K  19 " --> pdb=" O   LEU K  16 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 26 through 38
      removed outlier: 3.521A  pdb=" N   LEU K  30 " --> pdb=" O   SER K  26 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 39 through 44
    Processing helix  chain 'K' and resid 49 through 76
      removed outlier: 3.886A  pdb=" N   THR K  53 " --> pdb=" O   SER K  49 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 78 through 92
    Processing helix  chain 'K' and resid 94 through 111
      removed outlier: 3.696A  pdb=" N   GLN K  99 " --> pdb=" O   LEU K  95 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 111 through 128
      removed outlier: 3.578A  pdb=" N   THR K 128 " --> pdb=" O   VAL K 124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 129 through 133
    Processing helix  chain 'L' and resid 6 through 10
    Processing helix  chain 'L' and resid 12 through 17
    Processing helix  chain 'L' and resid 20 through 24
      removed outlier: 3.519A  pdb=" N   PHE L  23 " --> pdb=" O   PRO L  20 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE L  24 " --> pdb=" O   SER L  21 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 20 through 24'
    Processing helix  chain 'L' and resid 26 through 44
      removed outlier: 3.536A  pdb=" N   LEU L  30 " --> pdb=" O   SER L  26 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG L  39 " --> pdb=" O   SER L  35 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   GLU L  40 " --> pdb=" O   ALA L  36 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ALA L  41 " --> pdb=" O   LEU L  37 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER L  44 " --> pdb=" O   GLU L  40 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 3.852A  pdb=" N   THR L  53 " --> pdb=" O   SER L  49 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA L  54 " --> pdb=" O   PRO L  50 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 78 through 110
      removed outlier: 3.864A  pdb=" N   GLY L  94 " --> pdb=" O   ASN L  90 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   LEU L  95 " --> pdb=" O   THR L  91 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LYS L  96 " --> pdb=" O   ASN L  92 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 111 through 128
      removed outlier: 3.736A  pdb=" N   VAL L 120 " --> pdb=" O   ILE L 116 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 129 through 133

    907 hydrogen bonds defined for protein.
    2565 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: 3.58

  Time building geometry restraints manager: 3.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4258
        1.34 -     1.46: 2758
        1.46 -     1.58: 7015
        1.58 -     1.70: 1
        1.70 -     1.82: 108
  Bond restraints: 14140
  Sorted by residual:
  bond pdb=" CG  PRO A  45 "
       pdb=" CD  PRO A  45 "
    ideal  model  delta    sigma   weight residual
    1.503  1.406  0.097 3.40e-02 8.65e+02 8.18e+00
  bond pdb=" CB  PRO A  45 "
       pdb=" CG  PRO A  45 "
    ideal  model  delta    sigma   weight residual
    1.492  1.591 -0.099 5.00e-02 4.00e+02 3.93e+00
  bond pdb=" CB  GLU I  40 "
       pdb=" CG  GLU I  40 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.12e+00
  bond pdb=" CB  MET H  66 "
       pdb=" CG  MET H  66 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.11e-01
  bond pdb=" CA  PRO A  45 "
       pdb=" CB  PRO A  45 "
    ideal  model  delta    sigma   weight residual
    1.531  1.542 -0.011 1.22e-02 6.72e+03 7.85e-01
  ... (remaining 14135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 19118
        2.16 -     4.32: 213
        4.32 -     6.48: 21
        6.48 -     8.64: 0
        8.64 -    10.80: 8
  Bond angle restraints: 19360
  Sorted by residual:
  angle pdb=" CA  PRO A  45 "
        pdb=" N   PRO A  45 "
        pdb=" CD  PRO A  45 "
      ideal   model   delta    sigma   weight residual
     112.00  102.65    9.35 1.40e+00 5.10e-01 4.46e+01
  angle pdb=" N   PRO A  45 "
        pdb=" CD  PRO A  45 "
        pdb=" CG  PRO A  45 "
      ideal   model   delta    sigma   weight residual
     103.20   93.83    9.37 1.50e+00 4.44e-01 3.90e+01
  angle pdb=" CB  MET K   1 "
        pdb=" CG  MET K   1 "
        pdb=" SD  MET K   1 "
      ideal   model   delta    sigma   weight residual
     112.70  123.50  -10.80 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" CB  MET H  66 "
        pdb=" CG  MET H  66 "
        pdb=" SD  MET H  66 "
      ideal   model   delta    sigma   weight residual
     112.70  123.39  -10.69 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" CB  MET E  93 "
        pdb=" CG  MET E  93 "
        pdb=" SD  MET E  93 "
      ideal   model   delta    sigma   weight residual
     112.70  122.96  -10.26 3.00e+00 1.11e-01 1.17e+01
  ... (remaining 19355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 7145
       17.92 -    35.83: 897
       35.83 -    53.75: 236
       53.75 -    71.66: 38
       71.66 -    89.58: 10
  Dihedral angle restraints: 8326
    sinusoidal: 3277
      harmonic: 5049
  Sorted by residual:
  dihedral pdb=" CA  ASP L   2 "
           pdb=" CB  ASP L   2 "
           pdb=" CG  ASP L   2 "
           pdb=" OD1 ASP L   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.99   58.99     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CA  ASN C  90 "
           pdb=" C   ASN C  90 "
           pdb=" N   THR C  91 "
           pdb=" CA  THR C  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  THR I  91 "
           pdb=" C   THR I  91 "
           pdb=" N   ASN I  92 "
           pdb=" CA  ASN I  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.56  -16.44     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 8323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1490
       0.035 -    0.070: 540
       0.070 -    0.105: 116
       0.105 -    0.140: 40
       0.140 -    0.175: 5
  Chirality restraints: 2191
  Sorted by residual:
  chirality pdb=" CB  THR C  91 "
            pdb=" CA  THR C  91 "
            pdb=" OG1 THR C  91 "
            pdb=" CG2 THR C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CB  VAL H  86 "
            pdb=" CA  VAL H  86 "
            pdb=" CG1 VAL H  86 "
            pdb=" CG2 VAL H  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.11e-01
  chirality pdb=" CA  ASN C  90 "
            pdb=" N   ASN C  90 "
            pdb=" C   ASN C  90 "
            pdb=" CB  ASN C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.10e-01
  ... (remaining 2188 not shown)

  Planarity restraints: 2450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D  32 "   -0.009 2.00e-02 2.50e+03   1.84e-02 3.39e+00
        pdb=" CG  ASP D  32 "    0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASP D  32 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP D  32 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B   2 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.23e+00
        pdb=" CG  ASP B   2 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASP B   2 "    0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP B   2 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP J  71 "   -0.008 2.00e-02 2.50e+03   8.65e-03 1.87e+00
        pdb=" CG  TRP J  71 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP J  71 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP J  71 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP J  71 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP J  71 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP J  71 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP J  71 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP J  71 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP J  71 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2447 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 243
        2.69 -     3.25: 12968
        3.25 -     3.80: 20880
        3.80 -     4.35: 24555
        4.35 -     4.90: 44074
  Nonbonded interactions: 102720
  Sorted by model distance:
  nonbonded pdb=" O   VAL G  86 "
            pdb=" ND2 ASN G  90 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" O   SER L  87 "
            pdb=" OG1 THR L  91 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER L  26 "
            pdb=" OD1 ASP L  29 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   SER F  87 "
            pdb=" OG1 THR F  91 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG  SER H  26 "
            pdb=" OD1 ASP H  29 "
     model   vdw
     2.284 3.040
  ... (remaining 102715 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' and resid 1 through 142)
  selection = chain 'B'
  selection = chain 'C'
  selection = (chain 'D' and resid 1 through 142)
  selection = (chain 'E' and resid 1 through 142)
  selection = (chain 'F' and resid 1 through 142)
  selection = chain 'G'
  selection = (chain 'H' and resid 1 through 142)
  selection = (chain 'I' and resid 1 through 142)
  selection = (chain 'J' and resid 1 through 142)
  selection = (chain 'K' and resid 1 through 142)
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.270
  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:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     31.470
  Find NCS groups from input model:        0.640
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
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      :  0.003   0.099  14140  Z= 0.133
  Angle     :  0.568  10.804  19360  Z= 0.296
  Chirality :  0.039   0.175   2191
  Planarity :  0.004   0.034   2450
  Dihedral  : 16.783  89.576   5040
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 26.99 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.21), residues: 1691
  helix:  2.32 (0.15), residues: 1169
  sheet:  None (None), residues: 0
  loop :  0.33 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP J  71 
 HIS   0.003   0.001   HIS C 104 
 PHE   0.015   0.001   PHE F  97 
 TYR   0.012   0.001   TYR D  88 
 ARG   0.005   0.000   ARG I  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17029 (  907)
  hydrogen bonds       : angle       5.01192 ( 2565)
  covalent geometry    : bond        0.00306 (14140)
  covalent geometry    : angle       0.56839 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 304
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
REVERT: D  136 ASN cc_start: 0.8362 (p0) cc_final: 0.7881 (p0)
REVERT: J  136 ASN cc_start: 0.8293 (p0) cc_final: 0.7886 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 309
  average time/residue: 0.2750
  time to fit residues: 119.0819
Evaluate side-chains
  305 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 298
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain D residue   29 ASP
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain H residue  136 ASN
Chi-restraints excluded: chain J residue   13 VAL
Chi-restraints excluded: chain K residue   22 ASP
Chi-restraints excluded: chain L residue   70 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    4.9990
   chunk 127 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    0.4980
   chunk 85 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   chunk 131 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 80 optimal weight:    0.7980
   chunk 98 optimal weight:    9.9990
   chunk 152 optimal weight:    0.0570
   overall best weight:    1.2100

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

Flipped N/Q/H residues before XYZ refinement:
I  52 HIS
L  52 HIS
L  92 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.085043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.067952 restraints weight = 27592.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.067952 restraints weight = 27976.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.067952 restraints weight = 27976.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.0906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14140  Z= 0.117
  Angle     :  0.518   7.344  19360  Z= 0.271
  Chirality :  0.038   0.159   2191
  Planarity :  0.005   0.041   2450
  Dihedral  :  4.313  58.401   1872
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 25.15 %
    Favored  : 71.96 %
  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:  2.90 (0.21), residues: 1691
  helix:  2.52 (0.15), residues: 1178
  sheet:  None (None), residues: 0
  loop :  0.56 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  71 
 HIS   0.003   0.001   HIS K  52 
 PHE   0.010   0.001   PHE L  97 
 TYR   0.010   0.001   TYR D  88 
 ARG   0.002   0.000   ARG F  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04980 (  907)
  hydrogen bonds       : angle       4.01518 ( 2565)
  covalent geometry    : bond        0.00242 (14140)
  covalent geometry    : angle       0.51783 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 296
  time to evaluate  : 1.311 
Fit side-chains
REVERT: D    7 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8397 (tttm)
REVERT: D  136 ASN cc_start: 0.7994 (p0) cc_final: 0.7620 (p0)
REVERT: G   82 ARG cc_start: 0.7436 (mtm-85) cc_final: 0.6916 (mtt180)
REVERT: H   96 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7326 (mtpt)
REVERT: J   70 THR cc_start: 0.8997 (m) cc_final: 0.8632 (t)
REVERT: J  136 ASN cc_start: 0.8004 (p0) cc_final: 0.7546 (p0)
REVERT: K   47 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6489 (p-80)
REVERT: K   86 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8255 (p)
  outliers start: 44
  outliers final: 23
  residues processed: 327
  average time/residue: 0.2664
  time to fit residues: 123.3715
Evaluate side-chains
  309 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 283
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue  114 THR
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   47 HIS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain K residue   86 VAL
Chi-restraints excluded: chain L residue   44 SER
Chi-restraints excluded: chain L residue  141 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 121 optimal weight:    6.9990
   chunk 136 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
H 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.083405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.065476 restraints weight = 27980.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.065501 restraints weight = 27491.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.065514 restraints weight = 27301.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  14140  Z= 0.142
  Angle     :  0.518   7.159  19360  Z= 0.272
  Chirality :  0.039   0.165   2191
  Planarity :  0.005   0.061   2450
  Dihedral  :  3.829  30.453   1861
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.08 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.21), residues: 1691
  helix:  2.57 (0.15), residues: 1179
  sheet:  None (None), residues: 0
  loop :  0.46 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J  71 
 HIS   0.004   0.001   HIS C 104 
 PHE   0.014   0.001   PHE L  97 
 TYR   0.012   0.001   TYR D  88 
 ARG   0.005   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05463 (  907)
  hydrogen bonds       : angle       3.98229 ( 2565)
  covalent geometry    : bond        0.00332 (14140)
  covalent geometry    : angle       0.51753 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 288
  time to evaluate  : 1.622 
Fit side-chains
REVERT: D    7 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8468 (tttm)
REVERT: D  136 ASN cc_start: 0.8084 (p0) cc_final: 0.7698 (p0)
REVERT: G   82 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.6965 (mtt180)
REVERT: H   96 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7383 (mtpt)
REVERT: J   70 THR cc_start: 0.8933 (m) cc_final: 0.8602 (t)
REVERT: J  136 ASN cc_start: 0.8104 (p0) cc_final: 0.7690 (p0)
REVERT: K   47 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.6750 (p-80)
REVERT: K   86 VAL cc_start: 0.8507 (t) cc_final: 0.8260 (p)
  outliers start: 56
  outliers final: 40
  residues processed: 326
  average time/residue: 0.2768
  time to fit residues: 127.1962
Evaluate side-chains
  326 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 284
  time to evaluate  : 1.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   68 LEU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain H residue  136 ASN
Chi-restraints excluded: chain I residue    3 ILE
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   26 SER
Chi-restraints excluded: chain I residue  107 CYS
Chi-restraints excluded: chain I residue  114 THR
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   13 VAL
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   47 HIS
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   44 SER
Chi-restraints excluded: chain L residue  141 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 137 optimal weight:    7.9990
   chunk 140 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 159 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 128 optimal weight:    4.9990
   chunk 122 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
J  47 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.079280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.061242 restraints weight = 28570.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.061253 restraints weight = 28307.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.061253 restraints weight = 28212.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  14140  Z= 0.203
  Angle     :  0.572   5.954  19360  Z= 0.301
  Chirality :  0.042   0.164   2191
  Planarity :  0.005   0.043   2450
  Dihedral  :  4.012  29.099   1861
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.97 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.21), residues: 1691
  helix:  2.47 (0.15), residues: 1179
  sheet:  None (None), residues: 0
  loop :  0.27 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J  71 
 HIS   0.006   0.001   HIS J  47 
 PHE   0.019   0.002   PHE L  97 
 TYR   0.014   0.002   TYR D  88 
 ARG   0.005   0.000   ARG A  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06747 (  907)
  hydrogen bonds       : angle       4.09450 ( 2565)
  covalent geometry    : bond        0.00503 (14140)
  covalent geometry    : angle       0.57185 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 295
  time to evaluate  : 1.499 
Fit side-chains
REVERT: D    7 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8497 (tttm)
REVERT: D  136 ASN cc_start: 0.8190 (p0) cc_final: 0.7737 (p0)
REVERT: F   88 TYR cc_start: 0.8278 (t80) cc_final: 0.7994 (t80)
REVERT: G   82 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7053 (mtt180)
REVERT: J   70 THR cc_start: 0.8981 (m) cc_final: 0.8644 (t)
REVERT: J  136 ASN cc_start: 0.8291 (p0) cc_final: 0.7871 (p0)
REVERT: K   16 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9283 (tt)
REVERT: K   47 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7028 (p-80)
  outliers start: 75
  outliers final: 59
  residues processed: 351
  average time/residue: 0.2658
  time to fit residues: 134.1151
Evaluate side-chains
  346 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 284
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   49 SER
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 LYS
Chi-restraints excluded: chain F residue  126 ILE
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   16 LEU
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   68 LEU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue    3 ILE
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   26 SER
Chi-restraints excluded: chain I residue  114 THR
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   16 LEU
Chi-restraints excluded: chain K residue   47 HIS
Chi-restraints excluded: chain K residue   67 THR
Chi-restraints excluded: chain K residue   86 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 THR
Chi-restraints excluded: chain L residue   22 ASP
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   44 SER
Chi-restraints excluded: chain L residue   96 LYS
Chi-restraints excluded: chain L residue  141 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   chunk 144 optimal weight:    9.9990
   chunk 125 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   chunk 85 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 151 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
H 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.079947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.061980 restraints weight = 28535.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.061980 restraints weight = 28340.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.061980 restraints weight = 28339.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  14140  Z= 0.166
  Angle     :  0.553   7.851  19360  Z= 0.290
  Chirality :  0.040   0.155   2191
  Planarity :  0.005   0.043   2450
  Dihedral  :  3.992  28.322   1861
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 24.62 %
    Favored  : 70.65 %
  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:  2.70 (0.21), residues: 1691
  helix:  2.46 (0.15), residues: 1179
  sheet:  None (None), residues: 0
  loop :  0.23 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP J  71 
 HIS   0.004   0.001   HIS A 104 
 PHE   0.015   0.001   PHE L  97 
 TYR   0.012   0.002   TYR D  88 
 ARG   0.005   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06248 (  907)
  hydrogen bonds       : angle       4.05190 ( 2565)
  covalent geometry    : bond        0.00398 (14140)
  covalent geometry    : angle       0.55295 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 292
  time to evaluate  : 1.642 
Fit side-chains
REVERT: D    7 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8465 (tttm)
REVERT: D  136 ASN cc_start: 0.8223 (p0) cc_final: 0.7770 (p0)
REVERT: E   86 VAL cc_start: 0.8559 (t) cc_final: 0.8042 (p)
REVERT: G   82 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7004 (mtt180)
REVERT: H   96 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7499 (mtpt)
REVERT: J   70 THR cc_start: 0.8956 (m) cc_final: 0.8629 (t)
REVERT: J  136 ASN cc_start: 0.8314 (p0) cc_final: 0.7903 (p0)
REVERT: K   16 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9275 (tt)
REVERT: K   47 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7099 (p-80)
REVERT: K   86 VAL cc_start: 0.8435 (t) cc_final: 0.8160 (p)
  outliers start: 72
  outliers final: 58
  residues processed: 343
  average time/residue: 0.2669
  time to fit residues: 130.3116
Evaluate side-chains
  340 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 279
  time to evaluate  : 1.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 HIS
Chi-restraints excluded: chain A residue   66 MET
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   49 SER
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 LYS
Chi-restraints excluded: chain F residue  126 ILE
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   16 LEU
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   68 LEU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue  126 ILE
Chi-restraints excluded: chain H residue  136 ASN
Chi-restraints excluded: chain I residue    3 ILE
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   26 SER
Chi-restraints excluded: chain I residue  107 CYS
Chi-restraints excluded: chain I residue  114 THR
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain J residue   27 VAL
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   16 LEU
Chi-restraints excluded: chain K residue   47 HIS
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   22 ASP
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   44 SER
Chi-restraints excluded: chain L residue   96 LYS
Chi-restraints excluded: chain L residue  141 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0070
   chunk 103 optimal weight:    9.9990
   chunk 117 optimal weight:    0.8980
   chunk 142 optimal weight:    6.9990
   chunk 149 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 84 optimal weight:    8.9990
   chunk 87 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.083198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.065298 restraints weight = 28406.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.065394 restraints weight = 27777.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 15)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.065394 restraints weight = 27296.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  14140  Z= 0.112
  Angle     :  0.507   8.034  19360  Z= 0.264
  Chirality :  0.037   0.142   2191
  Planarity :  0.005   0.036   2450
  Dihedral  :  3.776  27.937   1861
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 26.13 %
    Favored  : 70.26 %
  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:  3.00 (0.21), residues: 1691
  helix:  2.64 (0.15), residues: 1176
  sheet:  None (None), residues: 0
  loop :  0.49 (0.29), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP J  71 
 HIS   0.003   0.000   HIS B  47 
 PHE   0.010   0.001   PHE G  97 
 TYR   0.013   0.001   TYR J  88 
 ARG   0.005   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04428 (  907)
  hydrogen bonds       : angle       3.89066 ( 2565)
  covalent geometry    : bond        0.00232 (14140)
  covalent geometry    : angle       0.50709 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 289
  time to evaluate  : 1.452 
Fit side-chains
REVERT: A  136 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7955 (p0)
REVERT: D    7 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8454 (tttm)
REVERT: D  136 ASN cc_start: 0.8114 (p0) cc_final: 0.7743 (p0)
REVERT: E   86 VAL cc_start: 0.8742 (t) cc_final: 0.8300 (p)
REVERT: G   82 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.6951 (mtt180)
REVERT: I   39 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7618 (tpp-160)
REVERT: J  136 ASN cc_start: 0.8240 (p0) cc_final: 0.7828 (p0)
REVERT: K   16 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9280 (tt)
REVERT: K   86 VAL cc_start: 0.8510 (t) cc_final: 0.8017 (p)
  outliers start: 55
  outliers final: 40
  residues processed: 329
  average time/residue: 0.2632
  time to fit residues: 123.1276
Evaluate side-chains
  325 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 282
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 HIS
Chi-restraints excluded: chain A residue   66 MET
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  136 ASN
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 LYS
Chi-restraints excluded: chain F residue  126 ILE
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   26 SER
Chi-restraints excluded: chain I residue  107 CYS
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   13 VAL
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   16 LEU
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain L residue   22 ASP
Chi-restraints excluded: chain L residue  126 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 131 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0170
   chunk 67 optimal weight:    2.9990
   chunk 135 optimal weight:    5.9990
   chunk 127 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0980
   overall best weight:    1.0022

-------------------------------------------------------------------------------
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 = 0.3041 r_free = 0.3041 target = 0.083775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.065938 restraints weight = 28489.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 15)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.065938 restraints weight = 27886.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.065938 restraints weight = 27886.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14140  Z= 0.110
  Angle     :  0.516   9.757  19360  Z= 0.264
  Chirality :  0.037   0.155   2191
  Planarity :  0.005   0.063   2450
  Dihedral  :  3.697  27.398   1861
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.48 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.07 (0.21), residues: 1691
  helix:  2.65 (0.15), residues: 1181
  sheet:  None (None), residues: 0
  loop :  0.62 (0.29), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L  71 
 HIS   0.002   0.000   HIS H 104 
 PHE   0.010   0.001   PHE G  97 
 TYR   0.024   0.001   TYR K  88 
 ARG   0.005   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 (  907)
  hydrogen bonds       : angle       3.86600 ( 2565)
  covalent geometry    : bond        0.00237 (14140)
  covalent geometry    : angle       0.51646 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 290
  time to evaluate  : 1.561 
Fit side-chains
REVERT: A  136 ASN cc_start: 0.8329 (p0) cc_final: 0.7898 (p0)
REVERT: C   39 ARG cc_start: 0.8290 (tpm170) cc_final: 0.8085 (tpp-160)
REVERT: C   90 ASN cc_start: 0.8597 (m110) cc_final: 0.8190 (m110)
REVERT: D    7 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8446 (tttm)
REVERT: D  136 ASN cc_start: 0.8077 (p0) cc_final: 0.7712 (p0)
REVERT: E   86 VAL cc_start: 0.8756 (t) cc_final: 0.8287 (p)
REVERT: G   64 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7227 (mt-10)
REVERT: G   82 ARG cc_start: 0.7491 (mtm-85) cc_final: 0.6925 (mtt180)
REVERT: H  136 ASN cc_start: 0.8175 (p0) cc_final: 0.7971 (p0)
REVERT: I   39 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7642 (tpp-160)
REVERT: I   76 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7355 (tp)
REVERT: J  136 ASN cc_start: 0.8197 (p0) cc_final: 0.7799 (p0)
REVERT: K   16 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9269 (tt)
REVERT: K   86 VAL cc_start: 0.8477 (t) cc_final: 0.7946 (p)
  outliers start: 57
  outliers final: 44
  residues processed: 329
  average time/residue: 0.2582
  time to fit residues: 120.6866
Evaluate side-chains
  330 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 283
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 HIS
Chi-restraints excluded: chain A residue   66 MET
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 LYS
Chi-restraints excluded: chain F residue  126 ILE
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   68 LEU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain I residue    3 ILE
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  107 CYS
Chi-restraints excluded: chain I residue  114 THR
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  132 TYR
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   16 LEU
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain L residue   22 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 138 optimal weight:    0.8980
   overall best weight:    3.1786

-------------------------------------------------------------------------------
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 = 0.2997 r_free = 0.2997 target = 0.081296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.063325 restraints weight = 28408.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.063325 restraints weight = 28102.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.063325 restraints weight = 28102.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14140  Z= 0.154
  Angle     :  0.575  10.205  19360  Z= 0.293
  Chirality :  0.040   0.147   2191
  Planarity :  0.005   0.064   2450
  Dihedral  :  3.814  25.784   1861
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 25.15 %
    Favored  : 70.65 %
  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:  2.96 (0.21), residues: 1691
  helix:  2.60 (0.15), residues: 1181
  sheet:  None (None), residues: 0
  loop :  0.47 (0.29), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F  71 
 HIS   0.004   0.001   HIS G 104 
 PHE   0.015   0.001   PHE L  97 
 TYR   0.014   0.001   TYR D  88 
 ARG   0.004   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05538 (  907)
  hydrogen bonds       : angle       3.94281 ( 2565)
  covalent geometry    : bond        0.00371 (14140)
  covalent geometry    : angle       0.57458 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 283
  time to evaluate  : 1.440 
Fit side-chains
REVERT: A  136 ASN cc_start: 0.8250 (p0) cc_final: 0.7869 (p0)
REVERT: C   90 ASN cc_start: 0.8658 (m110) cc_final: 0.8248 (m110)
REVERT: D    7 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8498 (tttm)
REVERT: D  136 ASN cc_start: 0.8129 (p0) cc_final: 0.7746 (p0)
REVERT: E   86 VAL cc_start: 0.8754 (t) cc_final: 0.8275 (p)
REVERT: G   82 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.7015 (mtt180)
REVERT: H  136 ASN cc_start: 0.8273 (p0) cc_final: 0.8000 (p0)
REVERT: I   76 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7346 (tp)
REVERT: J  136 ASN cc_start: 0.8251 (p0) cc_final: 0.7844 (p0)
REVERT: K   16 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9301 (tt)
REVERT: K   47 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7105 (p-80)
REVERT: K   86 VAL cc_start: 0.8443 (t) cc_final: 0.7917 (p)
REVERT: L   76 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6979 (tt)
  outliers start: 64
  outliers final: 49
  residues processed: 334
  average time/residue: 0.2556
  time to fit residues: 122.1783
Evaluate side-chains
  333 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 279
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 LYS
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   68 LEU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue    3 ILE
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  107 CYS
Chi-restraints excluded: chain I residue  114 THR
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain J residue   27 VAL
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   16 LEU
Chi-restraints excluded: chain K residue   47 HIS
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain L residue   22 ASP
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain L residue  126 ILE
Chi-restraints excluded: chain L residue  141 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 125 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 166 optimal weight:    0.7980
   chunk 92 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0570
   chunk 119 optimal weight:    6.9990
   chunk 152 optimal weight:    0.0020
   overall best weight:    0.9708

-------------------------------------------------------------------------------
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 = 0.3045 r_free = 0.3045 target = 0.083930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.066143 restraints weight = 28144.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.066143 restraints weight = 27579.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.066143 restraints weight = 27579.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14140  Z= 0.112
  Angle     :  0.545  11.080  19360  Z= 0.274
  Chirality :  0.037   0.149   2191
  Planarity :  0.005   0.064   2450
  Dihedral  :  3.683  25.311   1861
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 25.61 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.11 (0.21), residues: 1691
  helix:  2.67 (0.15), residues: 1181
  sheet:  None (None), residues: 0
  loop :  0.64 (0.29), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP I  71 
 HIS   0.002   0.000   HIS H 104 
 PHE   0.009   0.001   PHE G  97 
 TYR   0.016   0.001   TYR D  88 
 ARG   0.004   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04169 (  907)
  hydrogen bonds       : angle       3.85386 ( 2565)
  covalent geometry    : bond        0.00244 (14140)
  covalent geometry    : angle       0.54493 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 289
  time to evaluate  : 1.584 
Fit side-chains
REVERT: A  136 ASN cc_start: 0.8248 (p0) cc_final: 0.7883 (p0)
REVERT: C   90 ASN cc_start: 0.8677 (m110) cc_final: 0.8304 (m110)
REVERT: D    7 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8391 (tttm)
REVERT: D  136 ASN cc_start: 0.8064 (p0) cc_final: 0.7698 (p0)
REVERT: E   86 VAL cc_start: 0.8727 (t) cc_final: 0.8234 (p)
REVERT: G   64 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7112 (mt-10)
REVERT: G   82 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.6956 (mtt180)
REVERT: H  136 ASN cc_start: 0.8280 (p0) cc_final: 0.7982 (p0)
REVERT: I   39 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7673 (tpp-160)
REVERT: I   76 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7280 (tp)
REVERT: J  136 ASN cc_start: 0.8172 (p0) cc_final: 0.7766 (p0)
REVERT: K   16 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9288 (tt)
REVERT: K   86 VAL cc_start: 0.8509 (t) cc_final: 0.8021 (p)
REVERT: L   76 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6878 (tt)
  outliers start: 55
  outliers final: 44
  residues processed: 330
  average time/residue: 0.2585
  time to fit residues: 122.3665
Evaluate side-chains
  330 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 282
  time to evaluate  : 1.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 LYS
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   16 LEU
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   68 LEU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain I residue    3 ILE
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   16 LEU
Chi-restraints excluded: chain J residue   27 VAL
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  132 TYR
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   16 LEU
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   76 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 127 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 121 optimal weight:    2.9990
   chunk 154 optimal weight:    5.9990
   chunk 139 optimal weight:    0.4980
   chunk 150 optimal weight:    4.9990
   chunk 129 optimal weight:    0.9980
   chunk 111 optimal weight:    0.6980
   chunk 63 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
K  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.085157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.067359 restraints weight = 28077.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.067360 restraints weight = 27515.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.067360 restraints weight = 27506.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  14140  Z= 0.107
  Angle     :  0.550  11.331  19360  Z= 0.273
  Chirality :  0.037   0.174   2191
  Planarity :  0.004   0.069   2450
  Dihedral  :  3.558  24.214   1861
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.80 %
    Favored  : 70.52 %
  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:  3.19 (0.21), residues: 1691
  helix:  2.70 (0.15), residues: 1181
  sheet:  None (None), residues: 0
  loop :  0.77 (0.30), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  62 
 HIS   0.002   0.000   HIS A  52 
 PHE   0.011   0.001   PHE G  97 
 TYR   0.016   0.001   TYR D  88 
 ARG   0.005   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (  907)
  hydrogen bonds       : angle       3.82279 ( 2565)
  covalent geometry    : bond        0.00236 (14140)
  covalent geometry    : angle       0.55028 (19360)

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

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

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3382 Ramachandran restraints generated.
    1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 282
  time to evaluate  : 1.455 
Fit side-chains
REVERT: A  136 ASN cc_start: 0.8229 (p0) cc_final: 0.7839 (p0)
REVERT: C   90 ASN cc_start: 0.8717 (m110) cc_final: 0.8370 (m110)
REVERT: D    7 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8412 (tttm)
REVERT: D  136 ASN cc_start: 0.7986 (p0) cc_final: 0.7640 (p0)
REVERT: E   86 VAL cc_start: 0.8678 (t) cc_final: 0.8209 (p)
REVERT: G   82 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.6953 (mtt180)
REVERT: H  136 ASN cc_start: 0.8313 (p0) cc_final: 0.7997 (p0)
REVERT: I   39 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7736 (tpp-160)
REVERT: I   76 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7237 (tp)
REVERT: J  136 ASN cc_start: 0.8102 (p0) cc_final: 0.7705 (p0)
REVERT: K   86 VAL cc_start: 0.8459 (t) cc_final: 0.7977 (p)
REVERT: L   76 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6870 (tt)
  outliers start: 56
  outliers final: 45
  residues processed: 323
  average time/residue: 0.2644
  time to fit residues: 122.2572
Evaluate side-chains
  323 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 275
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   47 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   38 TYR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   75 ASN
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain D residue    7 LYS
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain E residue   14 GLU
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain F residue   14 GLU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 LYS
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   38 TYR
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   16 LEU
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   68 LEU
Chi-restraints excluded: chain H residue   76 LEU
Chi-restraints excluded: chain I residue    3 ILE
Chi-restraints excluded: chain I residue   18 PHE
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   93 MET
Chi-restraints excluded: chain I residue  107 CYS
Chi-restraints excluded: chain I residue  114 THR
Chi-restraints excluded: chain I residue  126 ILE
Chi-restraints excluded: chain I residue  142 THR
Chi-restraints excluded: chain J residue   27 VAL
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue   65 LEU
Chi-restraints excluded: chain J residue  132 TYR
Chi-restraints excluded: chain K residue   12 THR
Chi-restraints excluded: chain K residue   27 VAL
Chi-restraints excluded: chain K residue   84 LEU
Chi-restraints excluded: chain L residue   27 VAL
Chi-restraints excluded: chain L residue   76 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 128 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 120 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3033 r_free = 0.3033 target = 0.083263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.065479 restraints weight = 28180.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.065479 restraints weight = 27528.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.065479 restraints weight = 27528.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14140  Z= 0.124
  Angle     :  0.567  11.145  19360  Z= 0.283
  Chirality :  0.039   0.204   2191
  Planarity :  0.005   0.068   2450
  Dihedral  :  3.608  23.215   1861
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 26.53 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.10 (0.21), residues: 1691
  helix:  2.65 (0.15), residues: 1181
  sheet:  None (None), residues: 0
  loop :  0.70 (0.29), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 102 
 HIS   0.003   0.001   HIS G 104 
 PHE   0.011   0.001   PHE G  97 
 TYR   0.016   0.001   TYR D  88 
 ARG   0.007   0.000   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04475 (  907)
  hydrogen bonds       : angle       3.87453 ( 2565)
  covalent geometry    : bond        0.00290 (14140)
  covalent geometry    : angle       0.56651 (19360)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4317.64 seconds
wall clock time: 77 minutes 52.76 seconds (4672.76 seconds total)