Starting phenix.real_space_refine
on Sat May 17 07:14:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j8m_61231/05_2025/9j8m_61231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j8m_61231/05_2025/9j8m_61231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j8m_61231/05_2025/9j8m_61231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j8m_61231/05_2025/9j8m_61231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j8m_61231/05_2025/9j8m_61231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j8m_61231/05_2025/9j8m_61231.cif"
  }
  resolution = 3.82
  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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     368      5.49       5
     S      27      5.16       5
     C    8796      2.51       5
     N    2945      2.21       5
     O    3695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15831
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 75}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 805
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 708
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 3753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 3753
          Classifications: {'DNA': 184}
          Link IDs: {'rna3p': 183}
    Chain: "J"
      Number of atoms: 3791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 3791
          Classifications: {'DNA': 184}
          Link IDs: {'rna3p': 183}
    Chain: "K"
      Number of atoms: 697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 697
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 85}
    Chain: "L"
      Number of atoms: 697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 697
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 85}
    Chain: "M"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 928
          Classifications: {'peptide': 119}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ARG M 453 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG M 453 " occ=0.50
  Time building chain proxies: 9.42, per 1000 atoms: 0.60
  Number of scatterers: 15831
  At special positions: 0
  Unit cell: (167.48, 117.66, 145.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P     368     15.00
     O    3695      8.00
     N    2945      7.00
     C    8796      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: 3.94
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 13 sheets defined
      66.7% alpha, 6.9% beta
      184 base pairs and 311 stacking pairs defined.
    Time for finding SS restraints: 8.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.530A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.531A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.686A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.581A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.501A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.504A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.620A  pdb=" N   ALA D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.569A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 4.009A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.911A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.605A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 72
      removed outlier: 3.728A  pdb=" N   ASP G  72 " --> pdb=" O   ASN G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
    Processing helix  chain 'K' and resid 4 through 13
      removed outlier: 3.950A  pdb=" N   GLU K  13 " --> pdb=" O   ASP K   9 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 19 through 23
    Processing helix  chain 'K' and resid 27 through 38
    Processing helix  chain 'K' and resid 41 through 52
    Processing helix  chain 'K' and resid 55 through 68
    Processing helix  chain 'K' and resid 70 through 88
    Processing helix  chain 'L' and resid 4 through 13
      removed outlier: 4.030A  pdb=" N   GLU L  13 " --> pdb=" O   ASP L   9 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 19 through 23
    Processing helix  chain 'L' and resid 27 through 38
    Processing helix  chain 'L' and resid 41 through 52
    Processing helix  chain 'L' and resid 55 through 68
    Processing helix  chain 'L' and resid 70 through 89
    Processing helix  chain 'M' and resid 501 through 503
      No H-bonds generated for 'chain 'M' and resid 501 through 503'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.558A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.373A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.384A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.349A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 8.000A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'M' and resid 430 through 436
      removed outlier: 3.530A  pdb=" N   ALA M 539 " --> pdb=" O   LEU M 530 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'M' and resid 440 through 445
      removed outlier: 5.520A  pdb=" N   VAL M 442 " --> pdb=" O   ARG M 455 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ARG M 455 " --> pdb=" O   VAL M 442 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 462 through 463

    529 hydrogen bonds defined for protein.
    1551 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      473 hydrogen bonds
      942 hydrogen bond angles
      0 basepair planarities
      184 basepair parallelities
      311 stacking parallelities
  Total time for adding SS restraints: 6.78

  Time building geometry restraints manager: 4.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3182
        1.33 -     1.45: 5359
        1.45 -     1.57: 7558
        1.57 -     1.69: 734
        1.69 -     1.81: 41
  Bond restraints: 16874
  Sorted by residual:
  bond pdb=" O3'  DG J 102 "
       pdb=" P    DT J 103 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.50e-02 4.44e+03 9.37e+00
  bond pdb=" N   ASN M 466 "
       pdb=" CA  ASN M 466 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.39e-02 5.18e+03 5.47e+00
  bond pdb=" O3'  DC J  99 "
       pdb=" P    DG J 100 "
    ideal  model  delta    sigma   weight residual
    1.607  1.640 -0.033 1.50e-02 4.44e+03 4.71e+00
  bond pdb=" C3'  DT J 152 "
       pdb=" O3'  DT J 152 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.65e+00
  bond pdb=" CA  ILE F  29 "
       pdb=" CB  ILE F  29 "
    ideal  model  delta    sigma   weight residual
    1.540  1.524  0.016 1.36e-02 5.41e+03 1.32e+00
  ... (remaining 16869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 23533
        1.30 -     2.59: 782
        2.59 -     3.89: 38
        3.89 -     5.18: 7
        5.18 -     6.48: 3
  Bond angle restraints: 24363
  Sorted by residual:
  angle pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
      ideal   model   delta    sigma   weight residual
     113.43  109.23    4.20 1.09e+00 8.42e-01 1.49e+01
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     110.77  117.25   -6.48 1.93e+00 2.68e-01 1.13e+01
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     111.02  116.79   -5.77 1.86e+00 2.89e-01 9.63e+00
  angle pdb=" N   LYS G  74 "
        pdb=" CA  LYS G  74 "
        pdb=" CB  LYS G  74 "
      ideal   model   delta    sigma   weight residual
     113.65  110.10    3.55 1.47e+00 4.63e-01 5.84e+00
  angle pdb=" CA  ASN M 466 "
        pdb=" C   ASN M 466 "
        pdb=" O   ASN M 466 "
      ideal   model   delta    sigma   weight residual
     120.32  117.72    2.60 1.18e+00 7.18e-01 4.87e+00
  ... (remaining 24358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.45: 7534
       35.45 -    70.90: 1601
       70.90 -   106.35: 17
      106.35 -   141.80: 0
      141.80 -   177.25: 2
  Dihedral angle restraints: 9154
    sinusoidal: 6151
      harmonic: 3003
  Sorted by residual:
  dihedral pdb=" C4'  DT J 152 "
           pdb=" C3'  DT J 152 "
           pdb=" O3'  DT J 152 "
           pdb=" P    DC J 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.75  177.25     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J 118 "
           pdb=" C3'  DG J 118 "
           pdb=" O3'  DG J 118 "
           pdb=" P    DG J 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.54  144.46     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" N   LEU A  65 "
           pdb=" CA  LEU A  65 "
           pdb=" CB  LEU A  65 "
           pdb=" CG  LEU A  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.92   58.92     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 9151 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1722
       0.026 -    0.053: 777
       0.053 -    0.079: 165
       0.079 -    0.105: 57
       0.105 -    0.131: 21
  Chirality restraints: 2742
  Sorted by residual:
  chirality pdb=" P    DG J 100 "
            pdb=" OP1  DG J 100 "
            pdb=" OP2  DG J 100 "
            pdb=" O5'  DG J 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ASN M 466 "
            pdb=" N   ASN M 466 "
            pdb=" C   ASN M 466 "
            pdb=" CB  ASN M 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.88e-01
  chirality pdb=" CA  ILE G  79 "
            pdb=" N   ILE G  79 "
            pdb=" C   ILE G  79 "
            pdb=" CB  ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 2739 not shown)

  Planarity restraints: 1819
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I 113 "   -0.024 2.00e-02 2.50e+03   1.06e-02 3.08e+00
        pdb=" N9   DA I 113 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DA I 113 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I 113 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DA I 113 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I 113 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I 113 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I 113 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I 113 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I 113 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I 113 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  42 "   -0.021 2.00e-02 2.50e+03   9.50e-03 2.48e+00
        pdb=" N9   DA I  42 "    0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DA I  42 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA I  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I  42 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  42 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  42 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DA I  42 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  42 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  41 "   -0.019 2.00e-02 2.50e+03   8.18e-03 2.01e+00
        pdb=" N9   DG I  41 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DG I  41 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  41 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  41 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  41 "   -0.000 2.00e-02 2.50e+03
        pdb=" O6   DG I  41 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  41 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I  41 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  41 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  41 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  41 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1816 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2979
        2.79 -     3.32: 14177
        3.32 -     3.85: 30836
        3.85 -     4.37: 34903
        4.37 -     4.90: 50618
  Nonbonded interactions: 133513
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" NH2 ARG G  20 "
            pdb=" OP1  DT I  54 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" O   LEU A  61 "
            pdb=" NH2 ARG B  36 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.328 3.040
  ... (remaining 133508 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 133)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 25 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 15 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 34 through 124)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.250
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     42.170
  Find NCS groups from input model:        0.340
  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:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
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   0.046  16874  Z= 0.149
  Angle     :  0.521   6.479  24363  Z= 0.328
  Chirality :  0.032   0.131   2742
  Planarity :  0.003   0.031   1819
  Dihedral  : 26.318 177.245   7220
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  3.79 %
    Favored  : 94.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.02 (0.26), residues: 1025
  helix:  2.81 (0.20), residues: 657
  sheet:  2.21 (0.79), residues: 50
  loop :  0.22 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP M 498 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.006   0.001   PHE L  49 
 TYR   0.012   0.001   TYR G  57 
 ARG   0.002   0.000   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10776 ( 1002)
  hydrogen bonds       : angle       4.22333 ( 2493)
  covalent geometry    : bond        0.00294 (16874)
  covalent geometry    : angle       0.52122 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 TYR cc_start: 0.7640 (t80) cc_final: 0.7381 (t80)
REVERT: L    6 LYS cc_start: 0.6747 (tttm) cc_final: 0.6040 (mtmm)
  outliers start: 13
  outliers final: 6
  residues processed: 218
  average time/residue: 0.3746
  time to fit residues: 109.0496
Evaluate side-chains
  101 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain K residue   80 CYS
Chi-restraints excluded: chain L residue   32 LYS
Chi-restraints excluded: chain L residue   80 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 101 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 105 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   chunk 121 optimal weight:   30.0000
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  68 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
B  93 GLN
D  49 HIS
E  39 HIS
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
F  93 GLN
G 112 GLN
H  95 GLN
L   5 GLN
L   7 HIS
L  48 GLN
** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.053328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.036408 restraints weight = 127445.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.037233 restraints weight = 61366.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.037733 restraints weight = 40133.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  16874  Z= 0.226
  Angle     :  0.598   7.445  24363  Z= 0.352
  Chirality :  0.035   0.152   2742
  Planarity :  0.004   0.052   1819
  Dihedral  : 30.044 179.927   5176
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.79 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.26), residues: 1025
  helix:  2.63 (0.20), residues: 667
  sheet:  1.60 (0.80), residues: 50
  loop :  0.15 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP M 498 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.021   0.002   PHE L  59 
 TYR   0.019   0.002   TYR F  88 
 ARG   0.008   0.001   ARG K  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05174 ( 1002)
  hydrogen bonds       : angle       3.53835 ( 2493)
  covalent geometry    : bond        0.00498 (16874)
  covalent geometry    : angle       0.59813 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.7635 (mtt) cc_final: 0.7295 (mtt)
REVERT: B   84 MET cc_start: 0.8808 (mmm) cc_final: 0.8297 (mmm)
REVERT: C   91 GLU cc_start: 0.8667 (tp30) cc_final: 0.8255 (tp30)
REVERT: H   42 TYR cc_start: 0.8035 (t80) cc_final: 0.7806 (t80)
REVERT: K   10 PHE cc_start: 0.7065 (t80) cc_final: 0.6651 (t80)
REVERT: K   48 GLN cc_start: 0.8129 (mp10) cc_final: 0.7869 (mp10)
REVERT: K   82 ARG cc_start: 0.8894 (tmm-80) cc_final: 0.8311 (tpm170)
REVERT: L    6 LYS cc_start: 0.8677 (tttm) cc_final: 0.7971 (pttm)
REVERT: M  447 GLU cc_start: 0.8477 (mp0) cc_final: 0.7837 (mt-10)
REVERT: M  453 ARG cc_start: 0.8964 (ttm170) cc_final: 0.8690 (ttm110)
REVERT: M  470 LYS cc_start: 0.8385 (mmtm) cc_final: 0.8119 (mmtm)
REVERT: M  481 TYR cc_start: 0.8075 (t80) cc_final: 0.7817 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 123
  average time/residue: 0.2991
  time to fit residues: 53.4065
Evaluate side-chains
  99 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 133 optimal weight:    7.9990
   chunk 126 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   chunk 22 optimal weight:    0.0030
   chunk 102 optimal weight:   10.0000
   chunk 113 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   overall best weight:    2.7996

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.053278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.036365 restraints weight = 125939.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.037174 restraints weight = 60848.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.037691 restraints weight = 40038.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16874  Z= 0.187
  Angle     :  0.562   6.510  24363  Z= 0.332
  Chirality :  0.033   0.149   2742
  Planarity :  0.004   0.052   1819
  Dihedral  : 30.073 179.533   5168
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.56 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.26), residues: 1025
  helix:  2.68 (0.20), residues: 668
  sheet:  1.47 (0.80), residues: 50
  loop :  0.20 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP M 498 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.020   0.001   PHE L  59 
 TYR   0.012   0.002   TYR B  51 
 ARG   0.004   0.000   ARG M 482 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04284 ( 1002)
  hydrogen bonds       : angle       3.33118 ( 2493)
  covalent geometry    : bond        0.00407 (16874)
  covalent geometry    : angle       0.56151 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8855 (mmm) cc_final: 0.8429 (mmm)
REVERT: C   91 GLU cc_start: 0.8611 (tp30) cc_final: 0.8247 (tp30)
REVERT: E   97 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7112 (mt-10)
REVERT: H   42 TYR cc_start: 0.7900 (t80) cc_final: 0.7671 (t80)
REVERT: K   10 PHE cc_start: 0.7037 (t80) cc_final: 0.6635 (t80)
REVERT: K   56 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8636 (tm-30)
REVERT: K   82 ARG cc_start: 0.8961 (tmm-80) cc_final: 0.8677 (mmt180)
REVERT: L    6 LYS cc_start: 0.8748 (tttm) cc_final: 0.8100 (pttm)
REVERT: L   53 LYS cc_start: 0.7818 (tppt) cc_final: 0.7608 (mmmt)
REVERT: M  447 GLU cc_start: 0.8441 (mp0) cc_final: 0.7848 (mt-10)
REVERT: M  470 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7908 (mmtm)
  outliers start: 21
  outliers final: 12
  residues processed: 116
  average time/residue: 0.2952
  time to fit residues: 50.0118
Evaluate side-chains
  100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 54 optimal weight:    0.0570
   chunk 33 optimal weight:    6.9990
   chunk 120 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   chunk 121 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   overall best weight:    2.2104

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 517 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.053293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.036214 restraints weight = 125756.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.037037 restraints weight = 60955.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.037535 restraints weight = 40049.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  16874  Z= 0.169
  Angle     :  0.552   7.091  24363  Z= 0.327
  Chirality :  0.033   0.146   2742
  Planarity :  0.003   0.043   1819
  Dihedral  : 29.972 178.864   5168
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.20 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.27), residues: 1025
  helix:  2.76 (0.20), residues: 670
  sheet:  1.15 (0.79), residues: 50
  loop :  0.27 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP M 514 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.017   0.001   PHE L  59 
 TYR   0.013   0.001   TYR L  43 
 ARG   0.005   0.000   ARG L  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04074 ( 1002)
  hydrogen bonds       : angle       3.20008 ( 2493)
  covalent geometry    : bond        0.00366 (16874)
  covalent geometry    : angle       0.55236 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8850 (mmm) cc_final: 0.8449 (mmm)
REVERT: C   91 GLU cc_start: 0.8561 (tp30) cc_final: 0.8301 (tp30)
REVERT: H   42 TYR cc_start: 0.7854 (t80) cc_final: 0.7601 (t80)
REVERT: K   10 PHE cc_start: 0.6937 (t80) cc_final: 0.6565 (t80)
REVERT: K   49 PHE cc_start: 0.7809 (t80) cc_final: 0.6080 (t80)
REVERT: K   56 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8593 (tm-30)
REVERT: K   82 ARG cc_start: 0.9002 (tmm-80) cc_final: 0.8799 (mmt180)
REVERT: L    6 LYS cc_start: 0.8815 (tttm) cc_final: 0.8202 (ptpp)
REVERT: M  447 GLU cc_start: 0.8343 (mp0) cc_final: 0.7702 (mt-10)
REVERT: M  470 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7891 (mmtm)
REVERT: M  531 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8777 (mm)
  outliers start: 17
  outliers final: 9
  residues processed: 119
  average time/residue: 0.2729
  time to fit residues: 47.9050
Evaluate side-chains
  105 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   26 ILE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain M residue  531 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 125 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 71 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   chunk 128 optimal weight:    9.9990
   chunk 107 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.053158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.036275 restraints weight = 128290.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.037082 restraints weight = 62229.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.037574 restraints weight = 41095.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16874  Z= 0.195
  Angle     :  0.576   8.983  24363  Z= 0.338
  Chirality :  0.034   0.221   2742
  Planarity :  0.004   0.043   1819
  Dihedral  : 30.037 178.723   5167
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 14.47 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.26), residues: 1025
  helix:  2.66 (0.20), residues: 673
  sheet:  0.88 (0.79), residues: 49
  loop :  0.15 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP M 498 
 HIS   0.004   0.001   HIS L   7 
 PHE   0.018   0.002   PHE L  49 
 TYR   0.013   0.002   TYR B  51 
 ARG   0.010   0.000   ARG K  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04458 ( 1002)
  hydrogen bonds       : angle       3.24112 ( 2493)
  covalent geometry    : bond        0.00428 (16874)
  covalent geometry    : angle       0.57592 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8815 (mmm) cc_final: 0.8390 (mmm)
REVERT: C   91 GLU cc_start: 0.8542 (tp30) cc_final: 0.8297 (tp30)
REVERT: E   97 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7120 (mt-10)
REVERT: H   42 TYR cc_start: 0.7910 (t80) cc_final: 0.7670 (t80)
REVERT: K   10 PHE cc_start: 0.6921 (t80) cc_final: 0.6502 (t80)
REVERT: L    6 LYS cc_start: 0.8807 (tttm) cc_final: 0.8248 (ptpp)
REVERT: M  447 GLU cc_start: 0.8369 (mp0) cc_final: 0.7742 (mt-10)
  outliers start: 21
  outliers final: 18
  residues processed: 106
  average time/residue: 0.3012
  time to fit residues: 47.7725
Evaluate side-chains
  102 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   26 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   49 PHE
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 106 optimal weight:   20.0000
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 87 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  76 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.053609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.036788 restraints weight = 127148.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.037602 restraints weight = 61800.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.038095 restraints weight = 40723.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16874  Z= 0.156
  Angle     :  0.553   9.478  24363  Z= 0.324
  Chirality :  0.033   0.233   2742
  Planarity :  0.003   0.044   1819
  Dihedral  : 29.949 178.362   5167
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.47 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.27), residues: 1025
  helix:  2.79 (0.20), residues: 673
  sheet:  0.86 (0.81), residues: 49
  loop :  0.20 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP M 498 
 HIS   0.004   0.001   HIS L   7 
 PHE   0.019   0.001   PHE L  59 
 TYR   0.012   0.001   TYR L  43 
 ARG   0.004   0.000   ARG K  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 ( 1002)
  hydrogen bonds       : angle       3.08844 ( 2493)
  covalent geometry    : bond        0.00335 (16874)
  covalent geometry    : angle       0.55279 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   97 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7075 (mt-10)
REVERT: H   42 TYR cc_start: 0.7800 (t80) cc_final: 0.7541 (t80)
REVERT: K   10 PHE cc_start: 0.6869 (t80) cc_final: 0.6453 (t80)
REVERT: K   56 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8531 (tm-30)
REVERT: K   82 ARG cc_start: 0.9032 (tmm-80) cc_final: 0.8813 (mmt180)
REVERT: L    6 LYS cc_start: 0.8847 (tttm) cc_final: 0.8338 (ptpp)
REVERT: M  447 GLU cc_start: 0.8391 (mp0) cc_final: 0.7793 (mt-10)
REVERT: M  482 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8197 (tpp80)
  outliers start: 19
  outliers final: 17
  residues processed: 111
  average time/residue: 0.2904
  time to fit residues: 47.3875
Evaluate side-chains
  106 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   58 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   26 ILE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   49 PHE
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  518 ASN
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 123 optimal weight:   20.0000
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 468 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.053408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.036624 restraints weight = 126673.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.037457 restraints weight = 60747.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.037970 restraints weight = 39610.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16874  Z= 0.171
  Angle     :  0.561   8.812  24363  Z= 0.328
  Chirality :  0.033   0.230   2742
  Planarity :  0.004   0.044   1819
  Dihedral  : 29.948 178.098   5167
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.27 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.27), residues: 1025
  helix:  2.78 (0.20), residues: 674
  sheet:  0.99 (0.83), residues: 49
  loop :  0.24 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP M 498 
 HIS   0.004   0.001   HIS L   7 
 PHE   0.019   0.001   PHE L  49 
 TYR   0.012   0.001   TYR G  57 
 ARG   0.003   0.000   ARG K  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 ( 1002)
  hydrogen bonds       : angle       3.11600 ( 2493)
  covalent geometry    : bond        0.00371 (16874)
  covalent geometry    : angle       0.56099 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8827 (mmm) cc_final: 0.8463 (mmm)
REVERT: E   97 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7146 (mt-10)
REVERT: H   42 TYR cc_start: 0.7847 (t80) cc_final: 0.7596 (t80)
REVERT: H   93 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8521 (mm-30)
REVERT: K   10 PHE cc_start: 0.6911 (t80) cc_final: 0.6476 (t80)
REVERT: K   56 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8587 (tm-30)
REVERT: L    6 LYS cc_start: 0.8851 (tttm) cc_final: 0.8327 (ptpp)
REVERT: M  447 GLU cc_start: 0.8371 (mp0) cc_final: 0.7776 (mt-10)
REVERT: M  482 ARG cc_start: 0.8388 (tpp80) cc_final: 0.8165 (tpp80)
  outliers start: 20
  outliers final: 19
  residues processed: 111
  average time/residue: 0.2947
  time to fit residues: 47.7365
Evaluate side-chains
  109 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   26 ILE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   49 PHE
Chi-restraints excluded: chain M residue  445 VAL
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  518 ASN
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0670
   chunk 76 optimal weight:   10.0000
   chunk 114 optimal weight:   20.0000
   chunk 104 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    2.4126

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.053142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.036502 restraints weight = 126356.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.037308 restraints weight = 61484.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 78)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.037786 restraints weight = 40444.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  16874  Z= 0.174
  Angle     :  0.569   9.058  24363  Z= 0.332
  Chirality :  0.033   0.232   2742
  Planarity :  0.004   0.044   1819
  Dihedral  : 29.969 177.898   5167
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.38 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.26), residues: 1025
  helix:  2.79 (0.20), residues: 673
  sheet:  0.97 (0.82), residues: 49
  loop :  0.22 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  84 
 HIS   0.004   0.001   HIS L   7 
 PHE   0.020   0.001   PHE L  49 
 TYR   0.012   0.001   TYR L  43 
 ARG   0.010   0.000   ARG K  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 ( 1002)
  hydrogen bonds       : angle       3.11851 ( 2493)
  covalent geometry    : bond        0.00380 (16874)
  covalent geometry    : angle       0.56868 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 1.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8379 (mmp) cc_final: 0.8065 (mpp)
REVERT: B   84 MET cc_start: 0.8761 (mmm) cc_final: 0.8425 (mmm)
REVERT: E   97 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7113 (mt-10)
REVERT: H   42 TYR cc_start: 0.7822 (t80) cc_final: 0.7558 (t80)
REVERT: H   93 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8502 (mm-30)
REVERT: K   10 PHE cc_start: 0.7004 (t80) cc_final: 0.6601 (t80)
REVERT: K   40 ASP cc_start: 0.8560 (p0) cc_final: 0.8335 (p0)
REVERT: K   56 GLU cc_start: 0.8720 (tm-30) cc_final: 0.7399 (mp0)
REVERT: K   57 ASP cc_start: 0.9260 (t70) cc_final: 0.8937 (t70)
REVERT: L    6 LYS cc_start: 0.8787 (tttm) cc_final: 0.8319 (ptpp)
REVERT: M  447 GLU cc_start: 0.8350 (mp0) cc_final: 0.7753 (mt-10)
REVERT: M  482 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8149 (tpp80)
  outliers start: 20
  outliers final: 18
  residues processed: 105
  average time/residue: 0.2864
  time to fit residues: 44.8663
Evaluate side-chains
  105 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   26 ILE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain M residue  445 VAL
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  518 ASN
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 112 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9990
   chunk 120 optimal weight:    9.9990
   chunk 25 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 126 optimal weight:   20.0000
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.053566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.036925 restraints weight = 126817.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.037744 restraints weight = 61457.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.038232 restraints weight = 40321.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16874  Z= 0.150
  Angle     :  0.576  15.371  24363  Z= 0.331
  Chirality :  0.033   0.231   2742
  Planarity :  0.004   0.045   1819
  Dihedral  : 29.888 177.496   5167
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.30 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.03 (0.26), residues: 1025
  helix:  2.85 (0.20), residues: 673
  sheet:  1.00 (0.82), residues: 49
  loop :  0.22 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  84 
 HIS   0.004   0.001   HIS L   7 
 PHE   0.018   0.001   PHE L  49 
 TYR   0.011   0.001   TYR G  57 
 ARG   0.004   0.000   ARG K  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 ( 1002)
  hydrogen bonds       : angle       3.03655 ( 2493)
  covalent geometry    : bond        0.00321 (16874)
  covalent geometry    : angle       0.57558 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8759 (mmm) cc_final: 0.8437 (mmm)
REVERT: H   42 TYR cc_start: 0.7729 (t80) cc_final: 0.7426 (t80)
REVERT: H   93 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8457 (mm-30)
REVERT: K   10 PHE cc_start: 0.6999 (t80) cc_final: 0.6618 (t80)
REVERT: L    6 LYS cc_start: 0.8750 (tttm) cc_final: 0.8297 (ptpp)
REVERT: M  447 GLU cc_start: 0.8363 (mp0) cc_final: 0.7749 (mt-10)
REVERT: M  482 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8184 (tpp80)
  outliers start: 17
  outliers final: 16
  residues processed: 104
  average time/residue: 0.2816
  time to fit residues: 43.5313
Evaluate side-chains
  105 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   26 ILE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain M residue  445 VAL
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 106 optimal weight:   20.0000
   chunk 34 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 118 optimal weight:    8.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.053322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.036729 restraints weight = 127879.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.037532 restraints weight = 62287.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.038031 restraints weight = 41082.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16874  Z= 0.174
  Angle     :  0.585  15.137  24363  Z= 0.336
  Chirality :  0.033   0.231   2742
  Planarity :  0.004   0.044   1819
  Dihedral  : 29.921 177.506   5167
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.30 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.26), residues: 1025
  helix:  2.77 (0.20), residues: 673
  sheet:  0.99 (0.82), residues: 49
  loop :  0.18 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K  84 
 HIS   0.005   0.001   HIS L   7 
 PHE   0.019   0.001   PHE L  49 
 TYR   0.012   0.001   TYR G  57 
 ARG   0.007   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04073 ( 1002)
  hydrogen bonds       : angle       3.10358 ( 2493)
  covalent geometry    : bond        0.00380 (16874)
  covalent geometry    : angle       0.58453 (24363)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 TYR cc_start: 0.7792 (t80) cc_final: 0.7530 (t80)
REVERT: H   93 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8497 (mm-30)
REVERT: K   10 PHE cc_start: 0.7008 (t80) cc_final: 0.6619 (t80)
REVERT: L    6 LYS cc_start: 0.8735 (tttm) cc_final: 0.8275 (ptpp)
REVERT: M  447 GLU cc_start: 0.8373 (mp0) cc_final: 0.7758 (mt-10)
REVERT: M  482 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8173 (tpp80)
  outliers start: 18
  outliers final: 17
  residues processed: 101
  average time/residue: 0.2920
  time to fit residues: 43.7821
Evaluate side-chains
  103 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   26 ILE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain M residue  445 VAL
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   chunk 112 optimal weight:    7.9990
   chunk 121 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.052350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.035635 restraints weight = 127409.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.036428 restraints weight = 62772.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.036911 restraints weight = 41651.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  16874  Z= 0.239
  Angle     :  0.633  15.059  24363  Z= 0.361
  Chirality :  0.036   0.233   2742
  Planarity :  0.004   0.046   1819
  Dihedral  : 30.309 177.487   5167
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.30 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.26), residues: 1025
  helix:  2.34 (0.20), residues: 684
  sheet:  0.83 (0.81), residues: 49
  loop : -0.14 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP M 498 
 HIS   0.005   0.001   HIS L   7 
 PHE   0.018   0.002   PHE L  49 
 TYR   0.017   0.002   TYR B  51 
 ARG   0.007   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05257 ( 1002)
  hydrogen bonds       : angle       3.41702 ( 2493)
  covalent geometry    : bond        0.00529 (16874)
  covalent geometry    : angle       0.63291 (24363)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5205.45 seconds
wall clock time: 91 minutes 40.95 seconds (5500.95 seconds total)