Starting phenix.real_space_refine
on Sat Aug 23 13:55:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fk0_29247/08_2025/8fk0_29247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fk0_29247/08_2025/8fk0_29247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fk0_29247/08_2025/8fk0_29247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fk0_29247/08_2025/8fk0_29247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fk0_29247/08_2025/8fk0_29247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fk0_29247/08_2025/8fk0_29247.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.035
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      14      5.16       5
     C    8008      2.51       5
     N    2016      2.21       5
     O    2590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12628
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "B"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "C"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "I"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "D"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "J"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "E"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "K"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "F"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "L"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "G"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "M"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "H"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
    Chain: "N"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
  Time building chain proxies: 2.59, per 1000 atoms: 0.21
  Number of scatterers: 12628
  At special positions: 0
  Unit cell: (90.72, 89.64, 164.16, 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      14     16.00
     O    2590      8.00
     N    2016      7.00
     C    8008      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 581.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3220

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 27 sheets defined
      28.4% alpha, 37.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 34
      removed outlier: 3.684A  pdb=" N   GLY A  30 " --> pdb=" O   PHE A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
      removed outlier: 3.741A  pdb=" N   ARG A 105 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 108 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 34
    Processing helix  chain 'B' and resid 102 through 108
      removed outlier: 3.695A  pdb=" N   ARG B 105 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY B 106 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL B 108 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 34
      removed outlier: 3.758A  pdb=" N   THR C   6 " --> pdb=" O   SER C   2 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY C  34 " --> pdb=" O   GLY C  30 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 34
      removed outlier: 3.607A  pdb=" N   GLY I  30 " --> pdb=" O   PHE I  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 34
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 3.818A  pdb=" N   GLY D 106 " --> pdb=" O   THR D 103 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 34
      removed outlier: 3.760A  pdb=" N   GLY J  30 " --> pdb=" O   PHE J  26 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 102 through 108
      removed outlier: 3.657A  pdb=" N   GLY J 106 " --> pdb=" O   THR J 103 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL J 108 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 34
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 3.729A  pdb=" N   GLY E 106 " --> pdb=" O   THR E 103 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL E 108 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 34
    Processing helix  chain 'K' and resid 102 through 106
      removed outlier: 3.579A  pdb=" N   ARG K 105 " --> pdb=" O   THR K 102 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY K 106 " --> pdb=" O   THR K 103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 102 through 106'
    Processing helix  chain 'F' and resid 2 through 34
      removed outlier: 3.535A  pdb=" N   PHE F  29 " --> pdb=" O   ALA F  25 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY F  30 " --> pdb=" O   PHE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 103 through 108
      removed outlier: 3.762A  pdb=" N   VAL F 108 " --> pdb=" O   ARG F 105 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 34
    Processing helix  chain 'G' and resid 2 through 34
      removed outlier: 3.545A  pdb=" N   PHE G  26 " --> pdb=" O   VAL G  22 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY G  27 " --> pdb=" O   GLY G  23 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 104 through 108
      removed outlier: 3.839A  pdb=" N   VAL G 108 " --> pdb=" O   ARG G 105 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 34
      removed outlier: 3.831A  pdb=" N   GLY M  34 " --> pdb=" O   GLY M  30 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 103 through 108
      removed outlier: 3.579A  pdb=" N   GLY M 106 " --> pdb=" O   THR M 103 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL M 108 " --> pdb=" O   ARG M 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 34
      removed outlier: 3.548A  pdb=" N   PHE H  29 " --> pdb=" O   ALA H  25 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLY H  30 " --> pdb=" O   PHE H  26 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 108
      removed outlier: 3.995A  pdb=" N   GLY H 106 " --> pdb=" O   THR H 103 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL H 108 " --> pdb=" O   ARG H 105 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2 through 34
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40
      removed outlier: 4.118A  pdb=" N   SER A  77 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL A  78 " --> pdb=" O   THR A  67 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   THR A  67 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA A  44 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   THR A 131 " --> pdb=" O   ALA A  44 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   LEU A  46 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A  52 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40
      removed outlier: 6.207A  pdb=" N   ALA B  44 " --> pdb=" O   ILE B 129 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   THR B 131 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   LEU B  46 " --> pdb=" O   THR B 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40
      removed outlier: 3.650A  pdb=" N   ASN B  89 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER B  96 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   SER B  77 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   VAL B  78 " --> pdb=" O   THR B  67 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   THR B  67 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR B 115 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLU B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 40
      removed outlier: 3.533A  pdb=" N   ALA C  39 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ALA C  44 " --> pdb=" O   ILE C 129 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   THR C 131 " --> pdb=" O   ALA C  44 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   LEU C  46 " --> pdb=" O   THR C 131 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER C 110 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40
      removed outlier: 3.533A  pdb=" N   ALA C  39 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU C  57 " --> pdb=" O   ASN C  89 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 38 through 40
      removed outlier: 6.452A  pdb=" N   ALA I  44 " --> pdb=" O   ILE I 129 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   THR I 131 " --> pdb=" O   ALA I  44 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   LEU I  46 " --> pdb=" O   THR I 131 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLU I 122 " --> pdb=" O   LEU I 118 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR I  64 " --> pdb=" O   ILE I  84 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 38 through 40
      removed outlier: 3.573A  pdb=" N   ASN I  89 " --> pdb=" O   LEU I  57 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   SER I  77 " --> pdb=" O   SER I  96 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   VAL I  78 " --> pdb=" O   THR I  67 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   THR I  67 " --> pdb=" O   VAL I  78 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR I  64 " --> pdb=" O   ILE I  84 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 40
      removed outlier: 3.699A  pdb=" N   THR D  52 " --> pdb=" O   SER D  47 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   THR D 115 " --> pdb=" O   LEU D  70 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   THR D  64 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 40
      removed outlier: 3.867A  pdb=" N   ASN D  89 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER D  77 " --> pdb=" O   SER D  96 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   VAL D  78 " --> pdb=" O   THR D  67 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   THR D  67 " --> pdb=" O   VAL D  78 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   THR D  64 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 38 through 40
      removed outlier: 6.604A  pdb=" N   ALA J  44 " --> pdb=" O   ILE J 129 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   THR J 131 " --> pdb=" O   ALA J  44 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU J  46 " --> pdb=" O   THR J 131 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLU J 122 " --> pdb=" O   LEU J 118 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR J  64 " --> pdb=" O   ILE J  84 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'J' and resid 38 through 40
      removed outlier: 3.825A  pdb=" N   ASN J  89 " --> pdb=" O   LEU J  57 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER J  96 " --> pdb=" O   SER J  77 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER J  77 " --> pdb=" O   SER J  96 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   VAL J  78 " --> pdb=" O   THR J  67 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   THR J  67 " --> pdb=" O   VAL J  78 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR J  64 " --> pdb=" O   ILE J  84 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 38 through 40
    Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 40
    Processing sheet with id=AB5, first strand: chain 'K' and resid 38 through 40
      removed outlier: 3.603A  pdb=" N   ASN K  89 " --> pdb=" O   LEU K  57 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER K  77 " --> pdb=" O   SER K  96 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY K  68 " --> pdb=" O   ILE K 117 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU K 122 " --> pdb=" O   LEU K 118 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA K  44 " --> pdb=" O   ILE K 129 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   THR K 131 " --> pdb=" O   ALA K  44 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   LEU K  46 " --> pdb=" O   THR K 131 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR K  52 " --> pdb=" O   SER K  47 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'K' and resid 64 through 65
    Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 40
      removed outlier: 3.779A  pdb=" N   LEU F  57 " --> pdb=" O   ASN F  89 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASN F  89 " --> pdb=" O   LEU F  57 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER F  77 " --> pdb=" O   SER F  96 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   VAL F  78 " --> pdb=" O   THR F  67 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   THR F  67 " --> pdb=" O   VAL F  78 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY F  68 " --> pdb=" O   ILE F 117 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA F  44 " --> pdb=" O   ILE F 129 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   THR F 131 " --> pdb=" O   ALA F  44 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   LEU F  46 " --> pdb=" O   THR F 131 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR F  52 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 38 through 40
      removed outlier: 3.558A  pdb=" N   ALA L  39 " --> pdb=" O   LYS L  58 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   ALA L  44 " --> pdb=" O   ILE L 129 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   THR L 131 " --> pdb=" O   ALA L  44 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU L  46 " --> pdb=" O   THR L 131 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLY L  68 " --> pdb=" O   ILE L 117 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 38 through 40
      removed outlier: 3.558A  pdb=" N   ALA L  39 " --> pdb=" O   LYS L  58 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU L  57 " --> pdb=" O   ASN L  89 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ASN L  89 " --> pdb=" O   LEU L  57 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 64 through 65
      removed outlier: 3.631A  pdb=" N   THR L  64 " --> pdb=" O   ILE L  84 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 38 through 40
    Processing sheet with id=AC3, first strand: chain 'G' and resid 75 through 77
      removed outlier: 3.672A  pdb=" N   THR G 115 " --> pdb=" O   LEU G  70 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ALA G  44 " --> pdb=" O   ILE G 129 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   THR G 131 " --> pdb=" O   ALA G  44 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   LEU G  46 " --> pdb=" O   THR G 131 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR G  45 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR G  54 " --> pdb=" O   THR G  45 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER G  47 " --> pdb=" O   THR G  52 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   THR G  52 " --> pdb=" O   SER G  47 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'M' and resid 38 through 40
      removed outlier: 3.586A  pdb=" N   ALA M  39 " --> pdb=" O   LYS M  58 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL M  55 " --> pdb=" O   TYR M  91 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   TYR M  91 " --> pdb=" O   VAL M  55 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   SER M  96 " --> pdb=" O   SER M  77 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   SER M  77 " --> pdb=" O   SER M  96 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   VAL M  78 " --> pdb=" O   THR M  67 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   THR M  67 " --> pdb=" O   VAL M  78 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLY M  68 " --> pdb=" O   ILE M 117 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE M 117 " --> pdb=" O   GLY M  68 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU M 122 " --> pdb=" O   LEU M 118 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ALA M  44 " --> pdb=" O   ILE M 129 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   THR M 131 " --> pdb=" O   ALA M  44 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU M  46 " --> pdb=" O   THR M 131 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   THR M  52 " --> pdb=" O   SER M  47 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 38 through 40
    Processing sheet with id=AC6, first strand: chain 'H' and resid 75 through 76
      removed outlier: 3.729A  pdb=" N   THR H  64 " --> pdb=" O   ILE H  84 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'H' and resid 75 through 76
      removed outlier: 6.640A  pdb=" N   ALA H  44 " --> pdb=" O   ILE H 129 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   THR H 131 " --> pdb=" O   ALA H  44 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   LEU H  46 " --> pdb=" O   THR H 131 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   THR H  52 " --> pdb=" O   SER H  47 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'N' and resid 38 through 40
      removed outlier: 6.645A  pdb=" N   ALA N  44 " --> pdb=" O   ILE N 129 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   THR N 131 " --> pdb=" O   ALA N  44 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   LEU N  46 " --> pdb=" O   THR N 131 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU N 116 " --> pdb=" O   VAL N 124 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'N' and resid 38 through 40
      removed outlier: 3.935A  pdb=" N   LEU N  57 " --> pdb=" O   ASN N  89 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASN N  89 " --> pdb=" O   LEU N  57 " (cutoff:3.500A)

    751 hydrogen bonds defined for protein.
    2157 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3990
        1.34 -     1.46: 2823
        1.46 -     1.58: 5843
        1.58 -     1.70: 0
        1.70 -     1.82: 28
  Bond restraints: 12684
  Sorted by residual:
  bond pdb=" N   VAL K  66 "
       pdb=" CA  VAL K  66 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.23e-02 6.61e+03 1.38e+00
  bond pdb=" N   VAL N  66 "
       pdb=" CA  VAL N  66 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.23e-02 6.61e+03 1.38e+00
  bond pdb=" CG1 ILE N  16 "
       pdb=" CD1 ILE N  16 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.15e+00
  bond pdb=" CA  GLY G  76 "
       pdb=" C   GLY G  76 "
    ideal  model  delta    sigma   weight residual
    1.514  1.523 -0.008 8.20e-03 1.49e+04 1.06e+00
  bond pdb=" CG  ARG A 105 "
       pdb=" CD  ARG A 105 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.75e-01
  ... (remaining 12679 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 17026
        1.58 -     3.15: 305
        3.15 -     4.73: 44
        4.73 -     6.31: 6
        6.31 -     7.88: 7
  Bond angle restraints: 17388
  Sorted by residual:
  angle pdb=" C   SER C 101 "
        pdb=" N   THR C 102 "
        pdb=" CA  THR C 102 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" N   ILE A 100 "
        pdb=" CA  ILE A 100 "
        pdb=" C   ILE A 100 "
      ideal   model   delta    sigma   weight residual
     111.91  109.16    2.75 8.90e-01 1.26e+00 9.52e+00
  angle pdb=" N   VAL J  41 "
        pdb=" CA  VAL J  41 "
        pdb=" C   VAL J  41 "
      ideal   model   delta    sigma   weight residual
     112.96  110.57    2.39 1.00e+00 1.00e+00 5.69e+00
  angle pdb=" CB  MET B  81 "
        pdb=" CG  MET B  81 "
        pdb=" SD  MET B  81 "
      ideal   model   delta    sigma   weight residual
     112.70  119.59   -6.89 3.00e+00 1.11e-01 5.28e+00
  angle pdb=" CA  LEU N   8 "
        pdb=" CB  LEU N   8 "
        pdb=" CG  LEU N   8 "
      ideal   model   delta    sigma   weight residual
     116.30  108.42    7.88 3.50e+00 8.16e-02 5.07e+00
  ... (remaining 17383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 6827
       16.45 -    32.90: 393
       32.90 -    49.35: 55
       49.35 -    65.81: 7
       65.81 -    82.26: 12
  Dihedral angle restraints: 7294
    sinusoidal: 2226
      harmonic: 5068
  Sorted by residual:
  dihedral pdb=" CA  ASN F  89 "
           pdb=" CB  ASN F  89 "
           pdb=" CG  ASN F  89 "
           pdb=" OD1 ASN F  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -173.49  -66.51     2      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CG  ARG B 105 "
           pdb=" CD  ARG B 105 "
           pdb=" NE  ARG B 105 "
           pdb=" CZ  ARG B 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   50.99   39.01     2      1.50e+01 4.44e-03 8.45e+00
  dihedral pdb=" CA  PHE J  29 "
           pdb=" CB  PHE J  29 "
           pdb=" CG  PHE J  29 "
           pdb=" CD1 PHE J  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   35.07   54.93     2      2.00e+01 2.50e-03 8.04e+00
  ... (remaining 7291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1852
       0.037 -    0.075: 428
       0.075 -    0.112: 215
       0.112 -    0.149: 71
       0.149 -    0.187: 10
  Chirality restraints: 2576
  Sorted by residual:
  chirality pdb=" CG  LEU G  57 "
            pdb=" CB  LEU G  57 "
            pdb=" CD1 LEU G  57 "
            pdb=" CD2 LEU G  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.71e-01
  chirality pdb=" CB  VAL G  55 "
            pdb=" CA  VAL G  55 "
            pdb=" CG1 VAL G  55 "
            pdb=" CG2 VAL G  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.60e-01
  chirality pdb=" CB  ILE N  17 "
            pdb=" CA  ILE N  17 "
            pdb=" CG1 ILE N  17 "
            pdb=" CG2 ILE N  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.58e-01
  ... (remaining 2573 not shown)

  Planarity restraints: 2058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET N  81 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.36e+00
        pdb=" C   MET N  81 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   MET N  81 "    0.008 2.00e-02 2.50e+03
        pdb=" N   THR N  82 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN M  72 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" C   ASN M  72 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ASN M  72 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY M  73 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  29 "    0.009 2.00e-02 2.50e+03   8.39e-03 1.23e+00
        pdb=" CG  PHE B  29 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  29 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  29 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  29 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  29 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  29 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2055 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 139
        2.64 -     3.20: 12025
        3.20 -     3.77: 18557
        3.77 -     4.33: 24216
        4.33 -     4.90: 42452
  Nonbonded interactions: 97389
  Sorted by model distance:
  nonbonded pdb=" O   VAL E 108 "
            pdb=" OG  SER K 119 "
     model   vdw
     2.069 3.040
  nonbonded pdb=" O   ILE G 100 "
            pdb=" OG1 THR G 103 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OD1 ASN A  72 "
            pdb=" N   GLY A  73 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OD1 ASN H  74 "
            pdb=" OG  SER H  99 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" NE2 GLN H  40 "
            pdb=" O   GLY H  42 "
     model   vdw
     2.235 3.120
  ... (remaining 97384 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

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:             4.730
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.960
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
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   0.042  12684  Z= 0.137
  Angle     :  0.555   7.883  17388  Z= 0.311
  Chirality :  0.045   0.187   2576
  Planarity :  0.002   0.030   2058
  Dihedral  : 11.080  82.258   4074
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.35 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.20), residues: 1820
  helix:  2.72 (0.22), residues: 574
  sheet:  0.03 (0.19), residues: 742
  loop : -0.94 (0.23), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 105 
 TYR   0.007   0.001   TYR L  91 
 PHE   0.019   0.001   PHE B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (12684)
  covalent geometry    : angle       0.55526 (17388)
  hydrogen bonds       : bond        0.18857 (  732)
  hydrogen bonds       : angle       7.75688 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7435 (tpt170)
REVERT: C  110 SER cc_start: 0.9240 (m) cc_final: 0.8748 (t)
REVERT: F  125 THR cc_start: 0.9457 (t) cc_final: 0.9181 (m)
REVERT: G  120 ASN cc_start: 0.6126 (t0) cc_final: 0.5478 (m-40)
REVERT: M   89 ASN cc_start: 0.8807 (m110) cc_final: 0.7671 (m-40)
REVERT: H   59 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6328 (m-40)
REVERT: N   17 ILE cc_start: 0.7996 (mm) cc_final: 0.7795 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0657
  time to fit residues: 21.8942
Evaluate side-chains
  158 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0060
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.3980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:   10.0000
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
K  89 ASN
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.113183 restraints weight = 21406.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.113875 restraints weight = 14693.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.114494 restraints weight = 11717.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.115281 restraints weight = 10150.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.115412 restraints weight = 9234.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12684  Z= 0.114
  Angle     :  0.530   8.305  17388  Z= 0.287
  Chirality :  0.046   0.202   2576
  Planarity :  0.002   0.021   2058
  Dihedral  :  3.918  17.954   1878
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  7.77 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.19), residues: 1820
  helix:  2.94 (0.22), residues: 574
  sheet: -0.09 (0.20), residues: 658
  loop : -1.10 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 105 
 TYR   0.021   0.002   TYR M  91 
 PHE   0.015   0.001   PHE G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12684)
  covalent geometry    : angle       0.52961 (17388)
  hydrogen bonds       : bond        0.04225 (  732)
  hydrogen bonds       : angle       5.22140 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 190
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 ASN cc_start: 0.9119 (m-40) cc_final: 0.8910 (m-40)
REVERT: B  105 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7481 (tpt170)
REVERT: F   10 LEU cc_start: 0.9381 (mm) cc_final: 0.9099 (mt)
REVERT: F  125 THR cc_start: 0.9572 (t) cc_final: 0.9298 (m)
REVERT: H   40 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8133 (tm-30)
REVERT: N  120 ASN cc_start: 0.8259 (p0) cc_final: 0.7817 (p0)
  outliers start: 22
  outliers final: 12
  residues processed: 199
  average time/residue: 0.0973
  time to fit residues: 29.7822
Evaluate side-chains
  175 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain G residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 8 optimal weight:    0.0170
   chunk 112 optimal weight:    0.0870
   chunk 56 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 159 optimal weight:    0.3980
   chunk 138 optimal weight:    0.0020
   chunk 165 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 179 optimal weight:    0.3980
   chunk 103 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.1804

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

Flipped N/Q/H residues before XYZ refinement:
G 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.139566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.115705 restraints weight = 21412.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.116606 restraints weight = 15453.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117177 restraints weight = 12972.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.118826 restraints weight = 10451.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.118799 restraints weight = 8646.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  12684  Z= 0.094
  Angle     :  0.493   9.055  17388  Z= 0.262
  Chirality :  0.045   0.192   2576
  Planarity :  0.002   0.030   2058
  Dihedral  :  3.733  13.770   1876
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.19 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.20), residues: 1820
  helix:  2.99 (0.22), residues: 574
  sheet: -0.08 (0.20), residues: 658
  loop : -1.13 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 105 
 TYR   0.009   0.001   TYR D  91 
 PHE   0.010   0.001   PHE G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 (12684)
  covalent geometry    : angle       0.49324 (17388)
  hydrogen bonds       : bond        0.03486 (  732)
  hydrogen bonds       : angle       4.50961 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 ASN cc_start: 0.9112 (m-40) cc_final: 0.8910 (m-40)
REVERT: A  110 SER cc_start: 0.9201 (m) cc_final: 0.8748 (t)
REVERT: B  105 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7448 (tpt170)
REVERT: C   59 ASN cc_start: 0.8396 (t0) cc_final: 0.7558 (m-40)
REVERT: J   72 ASN cc_start: 0.6558 (p0) cc_final: 0.5714 (t0)
REVERT: J  105 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7959 (tpp80)
REVERT: E   65 GLN cc_start: 0.8072 (mm110) cc_final: 0.7784 (mt0)
REVERT: F   10 LEU cc_start: 0.9337 (mm) cc_final: 0.9042 (mt)
REVERT: F  125 THR cc_start: 0.9580 (t) cc_final: 0.9313 (m)
REVERT: L  127 SER cc_start: 0.9086 (t) cc_final: 0.8547 (p)
REVERT: G   81 MET cc_start: 0.6476 (tpt) cc_final: 0.5711 (mpp)
REVERT: H   19 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8063 (tp)
REVERT: N  120 ASN cc_start: 0.8221 (p0) cc_final: 0.7802 (p0)
  outliers start: 26
  outliers final: 15
  residues processed: 202
  average time/residue: 0.0962
  time to fit residues: 30.2009
Evaluate side-chains
  185 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain M residue   28 LEU
Chi-restraints excluded: chain M residue   29 PHE
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain N residue   28 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 156 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 158 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 178 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 131 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 120 ASN
H  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.112943 restraints weight = 21645.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.113714 restraints weight = 15028.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.114194 restraints weight = 12731.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115249 restraints weight = 10605.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.115321 restraints weight = 9314.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12684  Z= 0.119
  Angle     :  0.495   8.298  17388  Z= 0.266
  Chirality :  0.045   0.189   2576
  Planarity :  0.002   0.023   2058
  Dihedral  :  3.721  14.787   1876
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 11.23 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.19), residues: 1820
  helix:  2.93 (0.22), residues: 574
  sheet:  0.03 (0.20), residues: 658
  loop : -1.12 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 105 
 TYR   0.007   0.001   TYR K  91 
 PHE   0.010   0.001   PHE G  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (12684)
  covalent geometry    : angle       0.49484 (17388)
  hydrogen bonds       : bond        0.03545 (  732)
  hydrogen bonds       : angle       4.36772 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 177
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 ASN cc_start: 0.9146 (m-40) cc_final: 0.8905 (m-40)
REVERT: A  110 SER cc_start: 0.9290 (m) cc_final: 0.8855 (t)
REVERT: B  105 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7454 (tpt170)
REVERT: J  105 ARG cc_start: 0.8290 (mtp85) cc_final: 0.8018 (tpp80)
REVERT: E   65 GLN cc_start: 0.8147 (mm110) cc_final: 0.7821 (mt0)
REVERT: F   10 LEU cc_start: 0.9394 (mm) cc_final: 0.9100 (mt)
REVERT: F   91 TYR cc_start: 0.7529 (m-10) cc_final: 0.7086 (m-10)
REVERT: F  125 THR cc_start: 0.9602 (t) cc_final: 0.9380 (m)
REVERT: G   81 MET cc_start: 0.6424 (tpt) cc_final: 0.5618 (mpp)
REVERT: H   59 ASN cc_start: 0.6060 (OUTLIER) cc_final: 0.5542 (m-40)
REVERT: N   65 GLN cc_start: 0.7225 (tp-100) cc_final: 0.6847 (tp-100)
REVERT: N  120 ASN cc_start: 0.8300 (p0) cc_final: 0.7895 (p0)
  outliers start: 39
  outliers final: 26
  residues processed: 198
  average time/residue: 0.0962
  time to fit residues: 29.3170
Evaluate side-chains
  193 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue  132 SER
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain G residue  123 THR
Chi-restraints excluded: chain M residue   28 LEU
Chi-restraints excluded: chain M residue   29 PHE
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue   59 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 122 optimal weight:    8.9990
   chunk 164 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 141 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.109070 restraints weight = 21826.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.110108 restraints weight = 14904.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.110816 restraints weight = 11539.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.111287 restraints weight = 10621.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.111426 restraints weight = 9202.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12684  Z= 0.175
  Angle     :  0.545   9.723  17388  Z= 0.292
  Chirality :  0.046   0.197   2576
  Planarity :  0.002   0.023   2058
  Dihedral  :  3.905  17.780   1876
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 12.14 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.19), residues: 1820
  helix:  3.03 (0.22), residues: 532
  sheet: -0.16 (0.20), residues: 658
  loop : -1.11 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 105 
 TYR   0.009   0.001   TYR L  91 
 PHE   0.018   0.002   PHE G  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (12684)
  covalent geometry    : angle       0.54527 (17388)
  hydrogen bonds       : bond        0.04027 (  732)
  hydrogen bonds       : angle       4.49842 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 165
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9398 (m) cc_final: 0.9003 (t)
REVERT: B  105 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7418 (tpt170)
REVERT: J  105 ARG cc_start: 0.8359 (mtp85) cc_final: 0.8138 (tpp80)
REVERT: K   60 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9150 (m)
REVERT: F   91 TYR cc_start: 0.7604 (m-10) cc_final: 0.7243 (m-10)
REVERT: F  125 THR cc_start: 0.9625 (t) cc_final: 0.9380 (m)
REVERT: G   81 MET cc_start: 0.6364 (tpt) cc_final: 0.5726 (mpp)
REVERT: N   65 GLN cc_start: 0.7318 (tp-100) cc_final: 0.6985 (tp-100)
REVERT: N  120 ASN cc_start: 0.8379 (p0) cc_final: 0.8000 (p0)
  outliers start: 50
  outliers final: 34
  residues processed: 197
  average time/residue: 0.0928
  time to fit residues: 28.5708
Evaluate side-chains
  192 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain I residue  125 THR
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue  132 SER
Chi-restraints excluded: chain E residue   33 THR
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain G residue  123 THR
Chi-restraints excluded: chain M residue   29 PHE
Chi-restraints excluded: chain M residue   41 VAL
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 120 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 124 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 176 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 136 optimal weight:    8.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 ASN
G 120 ASN
H  40 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.130340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.106394 restraints weight = 21935.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.106835 restraints weight = 15896.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.107651 restraints weight = 12723.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.108300 restraints weight = 10813.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.108448 restraints weight = 9625.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12684  Z= 0.208
  Angle     :  0.579  10.621  17388  Z= 0.308
  Chirality :  0.047   0.183   2576
  Planarity :  0.002   0.025   2058
  Dihedral  :  4.118  18.835   1876
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.56 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.19), residues: 1820
  helix:  2.80 (0.22), residues: 532
  sheet: -0.34 (0.20), residues: 658
  loop : -1.23 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 105 
 TYR   0.008   0.002   TYR L  91 
 PHE   0.019   0.002   PHE G  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (12684)
  covalent geometry    : angle       0.57935 (17388)
  hydrogen bonds       : bond        0.04388 (  732)
  hydrogen bonds       : angle       4.62437 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 151
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 ASN cc_start: 0.9061 (m-40) cc_final: 0.8855 (m-40)
REVERT: A  110 SER cc_start: 0.9494 (m) cc_final: 0.9099 (t)
REVERT: B  105 ARG cc_start: 0.7935 (tpp80) cc_final: 0.7299 (tpt170)
REVERT: J  105 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8086 (tpp80)
REVERT: K   60 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9208 (m)
REVERT: F   91 TYR cc_start: 0.7813 (m-10) cc_final: 0.7531 (m-10)
REVERT: F  125 THR cc_start: 0.9638 (t) cc_final: 0.9347 (m)
REVERT: G   81 MET cc_start: 0.6443 (tpt) cc_final: 0.5912 (mpp)
REVERT: N  120 ASN cc_start: 0.8427 (p0) cc_final: 0.8018 (p0)
  outliers start: 48
  outliers final: 39
  residues processed: 183
  average time/residue: 0.0968
  time to fit residues: 27.4780
Evaluate side-chains
  187 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 147
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain I residue   69 VAL
Chi-restraints excluded: chain I residue  125 THR
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue   56 THR
Chi-restraints excluded: chain J residue  132 SER
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain G residue  123 THR
Chi-restraints excluded: chain M residue   32 PHE
Chi-restraints excluded: chain M residue   41 VAL
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 178 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 146 optimal weight:    0.8980
   chunk 134 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.133806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.109920 restraints weight = 21590.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.110858 restraints weight = 15366.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.111319 restraints weight = 12251.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.112302 restraints weight = 10462.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.112328 restraints weight = 9345.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12684  Z= 0.120
  Angle     :  0.506   9.379  17388  Z= 0.272
  Chirality :  0.045   0.179   2576
  Planarity :  0.002   0.017   2058
  Dihedral  :  3.859  17.032   1876
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.19 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.20), residues: 1820
  helix:  3.00 (0.23), residues: 532
  sheet: -0.28 (0.20), residues: 658
  loop : -1.21 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 105 
 TYR   0.005   0.001   TYR G  91 
 PHE   0.011   0.001   PHE G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (12684)
  covalent geometry    : angle       0.50634 (17388)
  hydrogen bonds       : bond        0.03716 (  732)
  hydrogen bonds       : angle       4.31624 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 161
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ASN cc_start: 0.9029 (m-40) cc_final: 0.8782 (m-40)
REVERT: A  110 SER cc_start: 0.9467 (m) cc_final: 0.9030 (t)
REVERT: B  105 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7229 (tpt170)
REVERT: J  105 ARG cc_start: 0.8362 (mtp85) cc_final: 0.8060 (tpp80)
REVERT: E  105 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.8011 (mtm-85)
REVERT: F   91 TYR cc_start: 0.7721 (m-10) cc_final: 0.7416 (m-10)
REVERT: F  125 THR cc_start: 0.9554 (t) cc_final: 0.9292 (p)
REVERT: N  120 ASN cc_start: 0.8368 (p0) cc_final: 0.7943 (p0)
  outliers start: 47
  outliers final: 34
  residues processed: 196
  average time/residue: 0.0970
  time to fit residues: 29.2366
Evaluate side-chains
  188 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain I residue   69 VAL
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue   56 THR
Chi-restraints excluded: chain J residue  132 SER
Chi-restraints excluded: chain E residue   35 GLN
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain M residue   41 VAL
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 160 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0870
   chunk 154 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   chunk 134 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 148 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.131276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.106600 restraints weight = 21758.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.108441 restraints weight = 14521.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.109718 restraints weight = 11004.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.110456 restraints weight = 9145.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.110927 restraints weight = 8065.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12684  Z= 0.174
  Angle     :  0.548   9.168  17388  Z= 0.294
  Chirality :  0.046   0.220   2576
  Planarity :  0.002   0.020   2058
  Dihedral  :  3.942  18.216   1876
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.67 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.19), residues: 1820
  helix:  2.89 (0.22), residues: 532
  sheet: -0.42 (0.20), residues: 658
  loop : -1.25 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 105 
 TYR   0.007   0.001   TYR L  91 
 PHE   0.013   0.001   PHE C  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (12684)
  covalent geometry    : angle       0.54847 (17388)
  hydrogen bonds       : bond        0.04011 (  732)
  hydrogen bonds       : angle       4.44025 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 152
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A   89 ASN cc_start: 0.9048 (m-40) cc_final: 0.8803 (m-40)
REVERT: A  110 SER cc_start: 0.9480 (m) cc_final: 0.9085 (t)
REVERT: B  105 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7335 (tpt170)
REVERT: I   72 ASN cc_start: 0.7915 (p0) cc_final: 0.7667 (p0)
REVERT: J  105 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7985 (tpp80)
REVERT: E  105 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.8050 (mtm-85)
REVERT: F   91 TYR cc_start: 0.7850 (m-10) cc_final: 0.7593 (m-10)
REVERT: F  125 THR cc_start: 0.9588 (t) cc_final: 0.9330 (m)
REVERT: L   81 MET cc_start: 0.7383 (ttm) cc_final: 0.6887 (mtp)
REVERT: G  120 ASN cc_start: 0.5273 (OUTLIER) cc_final: 0.4845 (m-40)
REVERT: N   16 ILE cc_start: 0.8742 (mm) cc_final: 0.8470 (mm)
REVERT: N   35 GLN cc_start: 0.7417 (pt0) cc_final: 0.7028 (pt0)
REVERT: N  120 ASN cc_start: 0.8339 (p0) cc_final: 0.7995 (p0)
  outliers start: 49
  outliers final: 43
  residues processed: 190
  average time/residue: 0.0879
  time to fit residues: 25.8610
Evaluate side-chains
  190 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain I residue   69 VAL
Chi-restraints excluded: chain I residue  125 THR
Chi-restraints excluded: chain D residue   29 PHE
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue  132 SER
Chi-restraints excluded: chain E residue   33 THR
Chi-restraints excluded: chain E residue   35 GLN
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain L residue   29 PHE
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain G residue  120 ASN
Chi-restraints excluded: chain M residue   32 PHE
Chi-restraints excluded: chain M residue   41 VAL
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 134 optimal weight:   10.0000
   chunk 141 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 138 optimal weight:    8.9990
   chunk 149 optimal weight:    0.3980
   chunk 167 optimal weight:    0.6980
   chunk 121 optimal weight:    6.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 120 ASN
M 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.129913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.106188 restraints weight = 22022.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.106633 restraints weight = 16132.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.106973 restraints weight = 13278.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.107022 restraints weight = 12018.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.107708 restraints weight = 11530.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12684  Z= 0.207
  Angle     :  0.589   9.101  17388  Z= 0.314
  Chirality :  0.047   0.182   2576
  Planarity :  0.002   0.025   2058
  Dihedral  :  4.103  20.295   1876
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.30 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.19), residues: 1820
  helix:  2.75 (0.22), residues: 532
  sheet: -0.52 (0.20), residues: 658
  loop : -1.34 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 105 
 TYR   0.008   0.001   TYR L  91 
 PHE   0.013   0.002   PHE G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (12684)
  covalent geometry    : angle       0.58941 (17388)
  hydrogen bonds       : bond        0.04300 (  732)
  hydrogen bonds       : angle       4.55879 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 147
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9500 (m) cc_final: 0.9121 (t)
REVERT: B  105 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7357 (tpt170)
REVERT: I   72 ASN cc_start: 0.7998 (p0) cc_final: 0.7738 (p0)
REVERT: J  105 ARG cc_start: 0.8333 (mtp85) cc_final: 0.8060 (tpp80)
REVERT: E  105 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8075 (mtm-85)
REVERT: F  125 THR cc_start: 0.9602 (t) cc_final: 0.9316 (m)
REVERT: L   81 MET cc_start: 0.7398 (ttm) cc_final: 0.6908 (mtp)
REVERT: G   81 MET cc_start: 0.6819 (tpt) cc_final: 0.6143 (mpp)
REVERT: M   84 ILE cc_start: 0.6751 (tt) cc_final: 0.6445 (pt)
REVERT: N   16 ILE cc_start: 0.8748 (mm) cc_final: 0.8469 (mm)
REVERT: N  120 ASN cc_start: 0.8337 (p0) cc_final: 0.7946 (p0)
  outliers start: 49
  outliers final: 43
  residues processed: 186
  average time/residue: 0.0902
  time to fit residues: 26.0918
Evaluate side-chains
  188 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 145
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain I residue   69 VAL
Chi-restraints excluded: chain I residue  125 THR
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue  132 SER
Chi-restraints excluded: chain E residue   33 THR
Chi-restraints excluded: chain E residue   35 GLN
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain L residue   29 PHE
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain M residue   32 PHE
Chi-restraints excluded: chain M residue   41 VAL
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain N residue   37 THR
Chi-restraints excluded: chain N residue   64 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 168 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 172 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 141 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.132220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.107963 restraints weight = 21757.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.108990 restraints weight = 15133.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.109284 restraints weight = 12131.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.110316 restraints weight = 10480.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.110352 restraints weight = 9493.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12684  Z= 0.123
  Angle     :  0.523   9.692  17388  Z= 0.278
  Chirality :  0.045   0.177   2576
  Planarity :  0.002   0.023   2058
  Dihedral  :  3.859  18.066   1876
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.85 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.20), residues: 1820
  helix:  4.57 (0.20), residues: 434
  sheet: -0.46 (0.20), residues: 658
  loop : -1.20 (0.20), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 105 
 TYR   0.006   0.001   TYR F  91 
 PHE   0.016   0.001   PHE C  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (12684)
  covalent geometry    : angle       0.52266 (17388)
  hydrogen bonds       : bond        0.03668 (  732)
  hydrogen bonds       : angle       4.28493 ( 2157)

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

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

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3640 Ramachandran restraints generated.
    1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 168
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9463 (m) cc_final: 0.9048 (t)
REVERT: B  105 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7315 (tpt170)
REVERT: I   72 ASN cc_start: 0.8092 (p0) cc_final: 0.7835 (p0)
REVERT: J  105 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8050 (tpp80)
REVERT: E  105 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7804 (mtm-85)
REVERT: F   91 TYR cc_start: 0.7865 (m-10) cc_final: 0.7535 (m-10)
REVERT: F  125 THR cc_start: 0.9536 (t) cc_final: 0.9255 (m)
REVERT: L   81 MET cc_start: 0.7425 (ttm) cc_final: 0.7159 (mtm)
REVERT: H   91 TYR cc_start: 0.8037 (m-80) cc_final: 0.7743 (m-80)
REVERT: N  120 ASN cc_start: 0.8295 (p0) cc_final: 0.7891 (p0)
  outliers start: 43
  outliers final: 40
  residues processed: 202
  average time/residue: 0.0816
  time to fit residues: 25.7248
Evaluate side-chains
  198 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 158
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   19 LEU
Chi-restraints excluded: chain I residue   69 VAL
Chi-restraints excluded: chain D residue   29 PHE
Chi-restraints excluded: chain D residue   70 LEU
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue   56 THR
Chi-restraints excluded: chain J residue  132 SER
Chi-restraints excluded: chain E residue   35 GLN
Chi-restraints excluded: chain E residue   37 THR
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   55 VAL
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue   71 ILE
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain L residue   29 PHE
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue   70 LEU
Chi-restraints excluded: chain L residue   89 ASN
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   91 TYR
Chi-restraints excluded: chain M residue   32 PHE
Chi-restraints excluded: chain M residue   41 VAL
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 144 optimal weight:    0.7980
   chunk 171 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0470
   chunk 159 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 172 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9990
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.134183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.110203 restraints weight = 21649.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.111301 restraints weight = 14962.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.111633 restraints weight = 12459.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.112591 restraints weight = 10467.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.112699 restraints weight = 9342.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12684  Z= 0.112
  Angle     :  0.510   9.528  17388  Z= 0.272
  Chirality :  0.045   0.176   2576
  Planarity :  0.002   0.030   2058
  Dihedral  :  3.746  15.699   1876
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.41 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.20), residues: 1820
  helix:  4.67 (0.20), residues: 434
  sheet: -0.49 (0.19), residues: 700
  loop : -1.09 (0.21), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 105 
 TYR   0.005   0.001   TYR G  91 
 PHE   0.013   0.001   PHE C  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (12684)
  covalent geometry    : angle       0.51012 (17388)
  hydrogen bonds       : bond        0.03455 (  732)
  hydrogen bonds       : angle       4.15603 ( 2157)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1725.00 seconds
wall clock time: 30 minutes 55.39 seconds (1855.39 seconds total)