Starting phenix.real_space_refine
on Thu May 15 01:17:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fk0_29247/05_2025/8fk0_29247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fk0_29247/05_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_29247/05_2025/8fk0_29247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fk0_29247/05_2025/8fk0_29247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fk0_29247/05_2025/8fk0_29247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fk0_29247/05_2025/8fk0_29247.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.00, per 1000 atoms: 0.63
  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: 3.22
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 2.07
  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: 4.41

  Time building geometry restraints manager: 3.76 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  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:                  0.010
  Normalize map: mean=0, sd=1:             2.880
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     32.500
  Find NCS groups from input model:        0.500
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.500
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.20), 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
 PHE   0.019   0.001   PHE B  29 
 TYR   0.007   0.001   TYR L  91 
 ARG   0.007   0.001   ARG B 105 

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

*********************** 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  : 1.213 
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: 0.1880
  time to fit residues: 61.3716
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  : 1.287 
-------------------------------------------------------------------------------
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 153 optimal weight:    1.9990
   chunk 137 optimal weight:    0.0000
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 142 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   chunk 165 optimal weight:    2.9990
   overall best weight:    1.3992

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

Flipped N/Q/H residues before XYZ refinement:
K  89 ASN
M  65 GLN
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.133000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.108818 restraints weight = 21598.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.109508 restraints weight = 15318.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.110071 restraints weight = 11829.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12684  Z= 0.166
  Angle     :  0.567   9.063  17388  Z= 0.305
  Chirality :  0.047   0.198   2576
  Planarity :  0.003   0.020   2058
  Dihedral  :  4.106  18.375   1878
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  7.63 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.19), residues: 1820
  helix:  2.76 (0.22), residues: 574
  sheet: -0.17 (0.20), residues: 616
  loop : -1.25 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE G  32 
 TYR   0.018   0.002   TYR M  91 
 ARG   0.005   0.001   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04677 (  732)
  hydrogen bonds       : angle       5.37596 ( 2157)
  covalent geometry    : bond        0.00383 (12684)
  covalent geometry    : angle       0.56656 (17388)

*********************** 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
  204 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
REVERT: B  105 ARG cc_start: 0.7947 (tpp80) cc_final: 0.7483 (tpt170)
REVERT: I    8 LEU cc_start: 0.9161 (tp) cc_final: 0.8918 (tp)
REVERT: E  105 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7758 (mtm-85)
REVERT: F   91 TYR cc_start: 0.7609 (m-10) cc_final: 0.7243 (m-10)
REVERT: F  125 THR cc_start: 0.9617 (t) cc_final: 0.9334 (m)
REVERT: H   32 PHE cc_start: 0.7719 (m-80) cc_final: 0.7475 (t80)
REVERT: N  120 ASN cc_start: 0.8406 (p0) cc_final: 0.7967 (p0)
  outliers start: 34
  outliers final: 22
  residues processed: 190
  average time/residue: 0.1963
  time to fit residues: 57.2110
Evaluate side-chains
  171 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
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   75 SER
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain I residue   14 SER
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  111 THR
Chi-restraints excluded: chain J residue  123 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 K residue   43 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
Chi-restraints excluded: chain N residue   29 PHE
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 177 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 129 optimal weight:    5.9990
   chunk 153 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.134596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.110701 restraints weight = 21716.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.111241 restraints weight = 15225.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.111848 restraints weight = 12071.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12684  Z= 0.122
  Angle     :  0.514   9.031  17388  Z= 0.276
  Chirality :  0.046   0.182   2576
  Planarity :  0.002   0.016   2058
  Dihedral  :  3.943  16.647   1876
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.10 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.19), residues: 1820
  helix:  2.83 (0.22), residues: 574
  sheet: -0.30 (0.20), residues: 658
  loop : -1.27 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.001   PHE C  29 
 TYR   0.007   0.001   TYR D  91 
 ARG   0.003   0.000   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04038 (  732)
  hydrogen bonds       : angle       4.83093 ( 2157)
  covalent geometry    : bond        0.00272 (12684)
  covalent geometry    : angle       0.51383 (17388)

*********************** 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
  196 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9400 (m) cc_final: 0.9007 (t)
REVERT: B  105 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7427 (tpt170)
REVERT: J  105 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8057 (tpp80)
REVERT: E  105 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7771 (mtm-85)
REVERT: F  125 THR cc_start: 0.9619 (t) cc_final: 0.9332 (m)
REVERT: G   81 MET cc_start: 0.6507 (tpt) cc_final: 0.5720 (mpp)
REVERT: N  120 ASN cc_start: 0.8299 (p0) cc_final: 0.7901 (p0)
  outliers start: 35
  outliers final: 25
  residues processed: 181
  average time/residue: 0.2114
  time to fit residues: 58.5956
Evaluate side-chains
  177 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
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 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  125 THR
Chi-restraints excluded: chain D residue   70 LEU
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   67 THR
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   37 THR
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   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
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 36 optimal weight:    0.4980
   chunk 164 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 141 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0370
   chunk 97 optimal weight:    2.9990
   chunk 173 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 122 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN
G 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.111170 restraints weight = 21468.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.111773 restraints weight = 15166.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.112138 restraints weight = 12710.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12684  Z= 0.115
  Angle     :  0.494   8.314  17388  Z= 0.265
  Chirality :  0.045   0.179   2576
  Planarity :  0.002   0.013   2058
  Dihedral  :  3.836  15.228   1876
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 12.21 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.19), residues: 1820
  helix:  2.83 (0.22), residues: 574
  sheet: -0.12 (0.20), residues: 658
  loop : -1.23 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE G  29 
 TYR   0.006   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  732)
  hydrogen bonds       : angle       4.48414 ( 2157)
  covalent geometry    : bond        0.00255 (12684)
  covalent geometry    : angle       0.49406 (17388)

*********************** 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
  210 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 167
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9381 (m) cc_final: 0.8967 (t)
REVERT: B  105 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7414 (tpt170)
REVERT: J  105 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8144 (tpp80)
REVERT: E  105 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7977 (mtm-85)
REVERT: K   60 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9077 (m)
REVERT: F   91 TYR cc_start: 0.7565 (m-80) cc_final: 0.7174 (m-10)
REVERT: F  125 THR cc_start: 0.9623 (t) cc_final: 0.9383 (m)
REVERT: H   40 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8426 (tm-30)
REVERT: N   65 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6559 (tp-100)
REVERT: N  120 ASN cc_start: 0.8300 (p0) cc_final: 0.7949 (p0)
  outliers start: 43
  outliers final: 27
  residues processed: 193
  average time/residue: 0.1976
  time to fit residues: 58.4163
Evaluate side-chains
  185 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
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   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  132 SER
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   60 THR
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   37 THR
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   28 LEU
Chi-restraints excluded: chain N residue   37 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 135 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 125 optimal weight:    0.0980
   chunk 131 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0670
   chunk 166 optimal weight:    2.9990
   chunk 114 optimal weight:    6.9990
   chunk 115 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 170 optimal weight:    0.5980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN
G 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.136667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.112930 restraints weight = 21383.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.113697 restraints weight = 14973.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.113992 restraints weight = 12250.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12684  Z= 0.097
  Angle     :  0.483   7.949  17388  Z= 0.258
  Chirality :  0.045   0.218   2576
  Planarity :  0.002   0.012   2058
  Dihedral  :  3.721  13.710   1876
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.94 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.20), residues: 1820
  helix:  2.90 (0.22), residues: 574
  sheet: -0.26 (0.20), residues: 658
  loop : -1.31 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE G  29 
 TYR   0.006   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  732)
  hydrogen bonds       : angle       4.23057 ( 2157)
  covalent geometry    : bond        0.00208 (12684)
  covalent geometry    : angle       0.48340 (17388)

*********************** 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
  217 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 180
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9317 (m) cc_final: 0.8907 (t)
REVERT: B  105 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7434 (tpt170)
REVERT: J  105 ARG cc_start: 0.8286 (mtp85) cc_final: 0.8081 (tpp80)
REVERT: E   65 GLN cc_start: 0.8114 (mm110) cc_final: 0.7708 (mt0)
REVERT: F   91 TYR cc_start: 0.7560 (m-80) cc_final: 0.7346 (m-10)
REVERT: F  125 THR cc_start: 0.9591 (t) cc_final: 0.9360 (m)
REVERT: H   19 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8090 (tp)
REVERT: H   40 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: N   65 GLN cc_start: 0.7016 (mm-40) cc_final: 0.6663 (tp-100)
REVERT: N  120 ASN cc_start: 0.8263 (p0) cc_final: 0.7843 (p0)
  outliers start: 37
  outliers final: 20
  residues processed: 205
  average time/residue: 0.1985
  time to fit residues: 62.6961
Evaluate side-chains
  183 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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 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   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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 169 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 116 optimal weight:    0.8980
   chunk 152 optimal weight:   30.0000
   chunk 161 optimal weight:    0.8980
   chunk 153 optimal weight:    0.2980
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.136663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.112816 restraints weight = 21763.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.113725 restraints weight = 16298.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115102 restraints weight = 12294.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12684  Z= 0.104
  Angle     :  0.492   8.104  17388  Z= 0.263
  Chirality :  0.045   0.194   2576
  Planarity :  0.002   0.023   2058
  Dihedral  :  3.681  13.858   1876
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.77 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.20), residues: 1820
  helix:  2.88 (0.22), residues: 574
  sheet: -0.10 (0.20), residues: 658
  loop : -1.20 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.001   PHE C  29 
 TYR   0.007   0.001   TYR G  91 
 ARG   0.004   0.001   ARG E 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  732)
  hydrogen bonds       : angle       4.11478 ( 2157)
  covalent geometry    : bond        0.00228 (12684)
  covalent geometry    : angle       0.49163 (17388)

*********************** 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
  214 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 171
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9364 (m) cc_final: 0.8922 (t)
REVERT: B  105 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7435 (tpt170)
REVERT: B  117 ILE cc_start: 0.9253 (mm) cc_final: 0.9039 (mt)
REVERT: J   72 ASN cc_start: 0.6654 (p0) cc_final: 0.5948 (t0)
REVERT: J  105 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8078 (tpp80)
REVERT: E   65 GLN cc_start: 0.7995 (mm110) cc_final: 0.7732 (mt0)
REVERT: F   10 LEU cc_start: 0.9324 (mm) cc_final: 0.9103 (mt)
REVERT: F  125 THR cc_start: 0.9568 (t) cc_final: 0.9330 (m)
REVERT: L  127 SER cc_start: 0.9105 (t) cc_final: 0.8655 (p)
REVERT: G   81 MET cc_start: 0.6764 (tpp) cc_final: 0.6317 (mpp)
REVERT: N   65 GLN cc_start: 0.7045 (mm-40) cc_final: 0.6654 (tp-100)
REVERT: N  120 ASN cc_start: 0.8309 (p0) cc_final: 0.7913 (p0)
  outliers start: 43
  outliers final: 31
  residues processed: 199
  average time/residue: 0.1971
  time to fit residues: 60.6614
Evaluate side-chains
  194 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
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   56 THR
Chi-restraints excluded: chain B residue   69 VAL
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 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   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   37 THR
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   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 44 optimal weight:    0.8980
   chunk 122 optimal weight:    8.9990
   chunk 172 optimal weight:    0.5980
   chunk 137 optimal weight:    0.8980
   chunk 170 optimal weight:    0.5980
   chunk 147 optimal weight:    0.0070
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 151 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0070
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.114884 restraints weight = 21313.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.115533 restraints weight = 14482.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.115877 restraints weight = 12164.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12684  Z= 0.092
  Angle     :  0.475   8.833  17388  Z= 0.255
  Chirality :  0.044   0.188   2576
  Planarity :  0.002   0.020   2058
  Dihedral  :  3.580  13.691   1876
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.88 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.20), residues: 1820
  helix:  3.22 (0.23), residues: 532
  sheet: -0.15 (0.19), residues: 700
  loop : -0.92 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE C  29 
 TYR   0.008   0.001   TYR F  91 
 ARG   0.005   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03125 (  732)
  hydrogen bonds       : angle       3.95987 ( 2157)
  covalent geometry    : bond        0.00194 (12684)
  covalent geometry    : angle       0.47508 (17388)

*********************** 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
  224 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 182
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9306 (m) cc_final: 0.8867 (t)
REVERT: B  105 ARG cc_start: 0.7943 (tpp80) cc_final: 0.7425 (tpt170)
REVERT: B  117 ILE cc_start: 0.9294 (mm) cc_final: 0.9089 (mt)
REVERT: I   72 ASN cc_start: 0.8048 (p0) cc_final: 0.7634 (p0)
REVERT: J   32 PHE cc_start: 0.9149 (m-80) cc_final: 0.8792 (m-80)
REVERT: J   72 ASN cc_start: 0.6609 (p0) cc_final: 0.5950 (t0)
REVERT: J  105 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8095 (tpp80)
REVERT: E   65 GLN cc_start: 0.7994 (mm110) cc_final: 0.7761 (mt0)
REVERT: F   10 LEU cc_start: 0.9309 (mm) cc_final: 0.9078 (mt)
REVERT: F   91 TYR cc_start: 0.7712 (m-10) cc_final: 0.7333 (m-10)
REVERT: F  125 THR cc_start: 0.9513 (t) cc_final: 0.9240 (p)
REVERT: L  127 SER cc_start: 0.9061 (t) cc_final: 0.8622 (p)
REVERT: H   19 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8025 (tp)
REVERT: N   29 PHE cc_start: 0.7469 (t80) cc_final: 0.7248 (t80)
REVERT: N   65 GLN cc_start: 0.6987 (mm-40) cc_final: 0.6704 (tp-100)
REVERT: N  120 ASN cc_start: 0.8273 (p0) cc_final: 0.7907 (p0)
  outliers start: 42
  outliers final: 28
  residues processed: 210
  average time/residue: 0.1966
  time to fit residues: 64.2108
Evaluate side-chains
  195 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
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 B residue   69 VAL
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 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 E residue   78 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  115 THR
Chi-restraints excluded: chain L residue   29 PHE
Chi-restraints excluded: chain L residue   37 THR
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 146 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 179 optimal weight:    7.9990
   chunk 73 optimal weight:    0.0970
   chunk 85 optimal weight:    0.0370
   chunk 169 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.5056

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.113628 restraints weight = 21452.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.114378 restraints weight = 15843.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.115911 restraints weight = 12169.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12684  Z= 0.096
  Angle     :  0.487   8.928  17388  Z= 0.258
  Chirality :  0.044   0.182   2576
  Planarity :  0.002   0.024   2058
  Dihedral  :  3.553  15.683   1876
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.78 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.20), residues: 1820
  helix:  3.23 (0.23), residues: 532
  sheet: -0.13 (0.19), residues: 700
  loop : -0.89 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE C  29 
 TYR   0.005   0.001   TYR G  91 
 ARG   0.006   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03128 (  732)
  hydrogen bonds       : angle       3.89118 ( 2157)
  covalent geometry    : bond        0.00209 (12684)
  covalent geometry    : angle       0.48735 (17388)

*********************** 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
  215 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 181
  time to evaluate  : 1.369 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9334 (m) cc_final: 0.8905 (t)
REVERT: B  105 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7437 (tpt170)
REVERT: J   32 PHE cc_start: 0.9130 (m-80) cc_final: 0.8786 (m-80)
REVERT: J   72 ASN cc_start: 0.6623 (p0) cc_final: 0.5968 (t0)
REVERT: J  105 ARG cc_start: 0.8258 (mtp85) cc_final: 0.8049 (tpp80)
REVERT: E   65 GLN cc_start: 0.7985 (mm110) cc_final: 0.7756 (mt0)
REVERT: K  114 LEU cc_start: 0.9310 (mp) cc_final: 0.9055 (mt)
REVERT: F   10 LEU cc_start: 0.9366 (mm) cc_final: 0.9097 (mt)
REVERT: F  125 THR cc_start: 0.9498 (t) cc_final: 0.9270 (p)
REVERT: L   81 MET cc_start: 0.7388 (ttm) cc_final: 0.6886 (mtp)
REVERT: L  127 SER cc_start: 0.9114 (t) cc_final: 0.8685 (p)
REVERT: G   81 MET cc_start: 0.6697 (tpt) cc_final: 0.6006 (mpp)
REVERT: H   19 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8016 (tp)
REVERT: N   65 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6749 (tp-100)
REVERT: N  120 ASN cc_start: 0.8269 (p0) cc_final: 0.7893 (p0)
  outliers start: 34
  outliers final: 27
  residues processed: 201
  average time/residue: 0.1962
  time to fit residues: 60.8380
Evaluate side-chains
  201 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
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 B residue   69 VAL
Chi-restraints excluded: chain C residue   69 VAL
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   56 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   71 ILE
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue   29 PHE
Chi-restraints excluded: chain L residue   37 THR
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 H residue   37 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 160 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 113 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 76 optimal weight:    0.5980
   chunk 137 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 121 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.133044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.108951 restraints weight = 21789.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.109974 restraints weight = 16717.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.110788 restraints weight = 12934.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12684  Z= 0.168
  Angle     :  0.544   8.424  17388  Z= 0.289
  Chirality :  0.046   0.184   2576
  Planarity :  0.002   0.021   2058
  Dihedral  :  3.807  16.373   1876
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.85 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.20), residues: 1820
  helix:  3.07 (0.22), residues: 532
  sheet: -0.26 (0.19), residues: 700
  loop : -0.94 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE C  29 
 TYR   0.008   0.001   TYR F  91 
 ARG   0.006   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  732)
  hydrogen bonds       : angle       4.20844 ( 2157)
  covalent geometry    : bond        0.00400 (12684)
  covalent geometry    : angle       0.54384 (17388)

*********************** 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
  200 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9427 (m) cc_final: 0.9011 (t)
REVERT: B  105 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7434 (tpt170)
REVERT: J  105 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8060 (tpp80)
REVERT: E   65 GLN cc_start: 0.8068 (mm110) cc_final: 0.7791 (mt0)
REVERT: F   91 TYR cc_start: 0.7861 (m-10) cc_final: 0.7481 (m-10)
REVERT: F  125 THR cc_start: 0.9573 (t) cc_final: 0.9324 (m)
REVERT: L   81 MET cc_start: 0.7440 (ttm) cc_final: 0.6917 (mtp)
REVERT: G   81 MET cc_start: 0.6805 (tpt) cc_final: 0.6133 (mpp)
REVERT: N  120 ASN cc_start: 0.8330 (p0) cc_final: 0.7962 (p0)
  outliers start: 36
  outliers final: 31
  residues processed: 187
  average time/residue: 0.1977
  time to fit residues: 56.7658
Evaluate side-chains
  190 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
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   56 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain C residue   69 VAL
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  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   43 THR
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 L residue   37 THR
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 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 139 optimal weight:    0.0170
   chunk 41 optimal weight:    0.9980
   chunk 169 optimal weight:    0.5980
   chunk 113 optimal weight:    0.0980
   chunk 86 optimal weight:    5.9990
   chunk 146 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 175 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9990
   chunk 135 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.136128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.112693 restraints weight = 21358.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.113182 restraints weight = 15156.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.113691 restraints weight = 12872.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12684  Z= 0.102
  Angle     :  0.498   9.027  17388  Z= 0.264
  Chirality :  0.045   0.185   2576
  Planarity :  0.002   0.024   2058
  Dihedral  :  3.644  14.977   1876
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.75 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.20), residues: 1820
  helix:  4.80 (0.20), residues: 434
  sheet: -0.18 (0.20), residues: 658
  loop : -0.98 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHE G  32 
 TYR   0.005   0.001   TYR F  91 
 ARG   0.006   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (  732)
  hydrogen bonds       : angle       4.00769 ( 2157)
  covalent geometry    : bond        0.00224 (12684)
  covalent geometry    : angle       0.49797 (17388)

********************** 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
  205 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.9399 (m) cc_final: 0.8957 (t)
REVERT: B  105 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7318 (tpt170)
REVERT: J   32 PHE cc_start: 0.9165 (m-80) cc_final: 0.8831 (m-80)
REVERT: J   72 ASN cc_start: 0.6764 (p0) cc_final: 0.6089 (t0)
REVERT: J  105 ARG cc_start: 0.8269 (mtp85) cc_final: 0.8027 (tpp80)
REVERT: E   65 GLN cc_start: 0.8040 (mm110) cc_final: 0.7786 (mt0)
REVERT: E  105 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7684 (mtm-85)
REVERT: F   91 TYR cc_start: 0.8079 (m-10) cc_final: 0.7669 (m-10)
REVERT: F  125 THR cc_start: 0.9546 (t) cc_final: 0.9309 (m)
REVERT: L   81 MET cc_start: 0.7428 (ttm) cc_final: 0.6917 (mtp)
REVERT: N  120 ASN cc_start: 0.8329 (p0) cc_final: 0.7863 (p0)
  outliers start: 33
  outliers final: 31
  residues processed: 192
  average time/residue: 0.1996
  time to fit residues: 58.7242
Evaluate side-chains
  198 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
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   56 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain C residue   69 VAL
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  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   43 THR
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 L residue   29 PHE
Chi-restraints excluded: chain L residue   37 THR
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 168 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0040
   chunk 167 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 69 optimal weight:    0.1980
   chunk 166 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 148 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.6194

-------------------------------------------------------------------------------
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 = 0.3574 r_free = 0.3574 target = 0.136232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.112732 restraints weight = 21360.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.113576 restraints weight = 15315.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.114884 restraints weight = 11793.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12684  Z= 0.104
  Angle     :  0.503   9.100  17388  Z= 0.266
  Chirality :  0.044   0.179   2576
  Planarity :  0.002   0.024   2058
  Dihedral  :  3.594  16.298   1876
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.41 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.20), residues: 1820
  helix:  4.81 (0.20), residues: 434
  sheet: -0.21 (0.20), residues: 658
  loop : -0.99 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.032   0.001   PHE C  29 
 TYR   0.005   0.001   TYR F  91 
 ARG   0.006   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03248 (  732)
  hydrogen bonds       : angle       3.94303 ( 2157)
  covalent geometry    : bond        0.00230 (12684)
  covalent geometry    : angle       0.50255 (17388)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3395.17 seconds
wall clock time: 61 minutes 50.40 seconds (3710.40 seconds total)