Starting phenix.real_space_refine
on Thu Jul 31 16:17:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn2_40610/07_2025/8sn2_40610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn2_40610/07_2025/8sn2_40610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2025/8sn2_40610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2025/8sn2_40610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2025/8sn2_40610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2025/8sn2_40610.cif"
  }
  resolution = 3.6
  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=   0.071
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7886      2.51       5
     N    2607      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13992
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 821
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
      Conformer: "B"
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          bond proxies already assigned to first conformer: 820
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12290  SG  CYS K  31      75.714  52.537  66.546  1.00 43.01           S
  ATOM  12440  SG  CYS K  51      76.545  50.797  63.302  1.00 44.84           S
  ATOM  12464  SG  CYS K  54      74.977  48.802  66.187  1.00 44.65           S
  ATOM  12181  SG  CYS K  16      84.103  56.800  57.767  1.00 44.32           S
  ATOM  12199  SG  CYS K  19      86.199  57.014  54.674  1.00 41.66           S
  ATOM  12329  SG  CYS K  36      83.580  59.855  55.726  1.00 45.57           S
  ATOM  12351  SG  CYS K  39      82.441  56.789  54.183  1.00 43.08           S

  Time building chain proxies: 8.77, per 1000 atoms: 0.63
  Number of scatterers: 13992
  At special positions: 0
  Unit cell: (108.896, 132.8, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2607      7.00
     C    7886      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 3.16
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
      Number of angles added : 9


  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 11 sheets defined
      65.5% alpha, 4.1% beta
      135 base pairs and 234 stacking pairs defined.
    Time for finding SS restraints: 5.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.922A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 114
      removed outlier: 3.554A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.563A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.866A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.989A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.513A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.783A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.527A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.526A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    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: 3.763A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.504A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 45 through 56
      removed outlier: 3.600A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.978A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.778A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.888A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    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 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.532A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.526A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
      removed outlier: 3.774A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 4.434A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 4.157A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.621A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.930A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.735A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.946A  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
      removed outlier: 3.519A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.924A  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 101 through 102
      removed outlier: 6.879A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.402A  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 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28
      removed outlier: 3.667A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25

    469 hydrogen bonds defined for protein.
    1391 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      234 stacking parallelities
  Total time for adding SS restraints: 4.52

  Time building geometry restraints manager: 3.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3379
        1.34 -     1.46: 4208
        1.46 -     1.58: 6637
        1.58 -     1.70: 586
        1.70 -     1.82: 47
  Bond restraints: 14857
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.61e+00
  bond pdb=" N   LYS L  63 "
       pdb=" CA  LYS L  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.55e-02 4.16e+03 1.12e+00
  bond pdb=" C   PHE L  62 "
       pdb=" N   LYS L  63 "
    ideal  model  delta    sigma   weight residual
    1.331  1.352 -0.021 2.07e-02 2.33e+03 1.06e+00
  bond pdb=" CB  ASN G 110 "
       pdb=" CG  ASN G 110 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.27e-01
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 9.15e-01
  ... (remaining 14852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 20633
        1.29 -     2.59: 629
        2.59 -     3.88: 59
        3.88 -     5.17: 18
        5.17 -     6.47: 4
  Bond angle restraints: 21343
  Sorted by residual:
  angle pdb=" CA  LYS K  46 "
        pdb=" CB  LYS K  46 "
        pdb=" CG  LYS K  46 "
      ideal   model   delta    sigma   weight residual
     114.10  119.63   -5.53 2.00e+00 2.50e-01 7.65e+00
  angle pdb=" CA  ARG L 136 "
        pdb=" CB  ARG L 136 "
        pdb=" CG  ARG L 136 "
      ideal   model   delta    sigma   weight residual
     114.10  118.58   -4.48 2.00e+00 2.50e-01 5.02e+00
  angle pdb=" CA  GLU K  25 "
        pdb=" CB  GLU K  25 "
        pdb=" CG  GLU K  25 "
      ideal   model   delta    sigma   weight residual
     114.10  118.57   -4.47 2.00e+00 2.50e-01 4.98e+00
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  119.17   -6.47 3.00e+00 1.11e-01 4.65e+00
  angle pdb=" CA  ASN G 110 "
        pdb=" CB  ASN G 110 "
        pdb=" CG  ASN G 110 "
      ideal   model   delta    sigma   weight residual
     112.60  114.63   -2.03 1.00e+00 1.00e+00 4.11e+00
  ... (remaining 21338 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 6883
       35.27 -    70.55: 1322
       70.55 -   105.82: 15
      105.82 -   141.09: 0
      141.09 -   176.36: 2
  Dihedral angle restraints: 8222
    sinusoidal: 5302
      harmonic: 2920
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.64  176.36     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.49  144.51     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CA  PHE L  62 "
           pdb=" C   PHE L  62 "
           pdb=" N   LYS L  63 "
           pdb=" CA  LYS L  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.85   18.15     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 8219 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1761
       0.031 -    0.062: 497
       0.062 -    0.093: 100
       0.093 -    0.123: 53
       0.123 -    0.154: 7
  Chirality restraints: 2418
  Sorted by residual:
  chirality pdb=" CB  ILE D  94 "
            pdb=" CA  ILE D  94 "
            pdb=" CG1 ILE D  94 "
            pdb=" CG2 ILE D  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.95e-01
  chirality pdb=" CB  ILE H  54 "
            pdb=" CA  ILE H  54 "
            pdb=" CG1 ILE H  54 "
            pdb=" CG2 ILE H  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  ILE F  46 "
            pdb=" N   ILE F  46 "
            pdb=" C   ILE F  46 "
            pdb=" CB  ILE F  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  ... (remaining 2415 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.70e+00
        pdb=" N   PRO E  43 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  83 "   -0.009 2.00e-02 2.50e+03   1.27e-02 3.23e+00
        pdb=" CG  TYR D  83 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  83 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  83 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  83 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  83 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D  83 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "    0.029 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO L  61 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 153
        2.63 -     3.19: 11417
        3.19 -     3.76: 24353
        3.76 -     4.33: 31481
        4.33 -     4.90: 47139
  Nonbonded interactions: 114543
  Sorted by model distance:
  nonbonded pdb=" OG  SER E  57 "
            pdb=" OE1 GLU E  59 "
     model   vdw
     2.058 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.175 2.496
  nonbonded pdb=" O   PRO L  61 "
            pdb=" NE1 TRP L  93 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" OH  TYR L  45 "
            pdb=" O   TYR L  74 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" OG  SER K  59 "
     model   vdw
     2.253 3.040
  ... (remaining 114538 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' and (resid 37 through 55 or resid 57 through 135))
  selection = (chain 'E' and (resid 37 through 55 or resid 57 through 135))
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 31 through 123)
  selection = chain 'H'
}

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=0.17 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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     38.550
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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   0.038  14867  Z= 0.140
  Angle     :  0.539   8.777  21358  Z= 0.314
  Chirality :  0.033   0.154   2418
  Planarity :  0.004   0.048   1687
  Dihedral  : 25.924 176.363   6330
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.27), residues: 982
  helix:  2.71 (0.22), residues: 612
  sheet:  0.72 (0.87), residues: 29
  loop : -0.86 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  77 
 HIS   0.005   0.001   HIS G  82 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.031   0.001   TYR D  83 
 ARG   0.007   0.000   ARG C  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00158 (    2)
  link_TRANS           : angle       0.52871 (    6)
  hydrogen bonds       : bond        0.10894 (  816)
  hydrogen bonds       : angle       3.82731 ( 2081)
  metal coordination   : bond        0.00363 (    8)
  metal coordination   : angle       4.82378 (    9)
  covalent geometry    : bond        0.00291 (14857)
  covalent geometry    : angle       0.53007 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8388 (mttp)
REVERT: C   41 GLU cc_start: 0.7306 (tt0) cc_final: 0.7102 (tt0)
REVERT: D   71 GLU cc_start: 0.8317 (tp30) cc_final: 0.8086 (tp30)
REVERT: F   25 ASN cc_start: 0.7791 (m110) cc_final: 0.7430 (m-40)
REVERT: H   59 MET cc_start: 0.8622 (tpp) cc_final: 0.8399 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2888
  time to fit residues: 74.9367
Evaluate side-chains
  141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0370
   chunk 49 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 110 optimal weight:    8.9990
   overall best weight:    1.3664

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
D  49 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.119405 restraints weight = 31019.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.123015 restraints weight = 61114.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123151 restraints weight = 25962.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14867  Z= 0.180
  Angle     :  0.594  15.834  21358  Z= 0.336
  Chirality :  0.035   0.179   2418
  Planarity :  0.005   0.041   1687
  Dihedral  : 29.333 175.551   4330
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.59 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.27), residues: 982
  helix:  2.58 (0.21), residues: 629
  sheet:  0.44 (0.94), residues: 30
  loop : -1.27 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  77 
 HIS   0.003   0.001   HIS G  82 
 PHE   0.013   0.002   PHE E  67 
 TYR   0.014   0.002   TYR K  84 
 ARG   0.005   0.000   ARG C  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00040 (    2)
  link_TRANS           : angle       0.43514 (    6)
  hydrogen bonds       : bond        0.05050 (  816)
  hydrogen bonds       : angle       3.23065 ( 2081)
  metal coordination   : bond        0.00733 (    8)
  metal coordination   : angle       7.16936 (    9)
  covalent geometry    : bond        0.00409 (14857)
  covalent geometry    : angle       0.57512 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.8991 (t70) cc_final: 0.8786 (t0)
REVERT: C   36 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8580 (mttp)
REVERT: D   71 GLU cc_start: 0.8530 (tp30) cc_final: 0.8249 (tp30)
REVERT: E   59 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7658 (pm20)
REVERT: F   25 ASN cc_start: 0.7994 (m110) cc_final: 0.7635 (m-40)
  outliers start: 13
  outliers final: 9
  residues processed: 153
  average time/residue: 0.2732
  time to fit residues: 59.8945
Evaluate side-chains
  152 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  104 LEU
Chi-restraints excluded: chain L residue  108 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 120 optimal weight:   10.0000
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.154639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.120716 restraints weight = 34528.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.124647 restraints weight = 69055.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.125695 restraints weight = 21968.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14867  Z= 0.169
  Angle     :  0.577  14.285  21358  Z= 0.329
  Chirality :  0.035   0.215   2418
  Planarity :  0.004   0.040   1687
  Dihedral  : 29.433 175.324   4330
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.35 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.27), residues: 982
  helix:  2.62 (0.21), residues: 622
  sheet:  0.53 (0.94), residues: 30
  loop : -1.31 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP L  93 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.010   0.002   PHE E  67 
 TYR   0.011   0.001   TYR K  84 
 ARG   0.004   0.000   ARG C  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00020 (    2)
  link_TRANS           : angle       0.27463 (    6)
  hydrogen bonds       : bond        0.04786 (  816)
  hydrogen bonds       : angle       3.13547 ( 2081)
  metal coordination   : bond        0.00616 (    8)
  metal coordination   : angle       6.80178 (    9)
  covalent geometry    : bond        0.00383 (14857)
  covalent geometry    : angle       0.55993 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8813 (m-10) cc_final: 0.8439 (m-10)
REVERT: C   36 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8522 (mttp)
REVERT: D   71 GLU cc_start: 0.8578 (tp30) cc_final: 0.8321 (tp30)
REVERT: E   59 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7774 (pm20)
REVERT: F   25 ASN cc_start: 0.8155 (m110) cc_final: 0.7761 (m-40)
REVERT: H   59 MET cc_start: 0.8805 (tpp) cc_final: 0.8171 (tpp)
  outliers start: 16
  outliers final: 13
  residues processed: 146
  average time/residue: 0.2795
  time to fit residues: 58.9705
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain L residue   80 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 118 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 112 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.151256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.119791 restraints weight = 38551.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.122326 restraints weight = 75241.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.124009 restraints weight = 21980.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  14867  Z= 0.212
  Angle     :  0.610  14.471  21358  Z= 0.347
  Chirality :  0.037   0.217   2418
  Planarity :  0.005   0.044   1687
  Dihedral  : 29.834 173.001   4330
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.92 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.27), residues: 982
  helix:  2.52 (0.21), residues: 616
  sheet:  0.53 (0.95), residues: 30
  loop : -1.36 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L  93 
 HIS   0.005   0.001   HIS G  31 
 PHE   0.012   0.002   PHE L  51 
 TYR   0.023   0.002   TYR D  83 
 ARG   0.003   0.000   ARG A 116 

Details of bonding type rmsd
  link_TRANS           : bond        0.00065 (    2)
  link_TRANS           : angle       0.21649 (    6)
  hydrogen bonds       : bond        0.05574 (  816)
  hydrogen bonds       : angle       3.24667 ( 2081)
  metal coordination   : bond        0.00760 (    8)
  metal coordination   : angle       7.31010 (    9)
  covalent geometry    : bond        0.00497 (14857)
  covalent geometry    : angle       0.59162 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8868 (m-10) cc_final: 0.8544 (m-10)
REVERT: C   35 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7738 (mtt180)
REVERT: C   36 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8543 (mttp)
REVERT: F   25 ASN cc_start: 0.8212 (m110) cc_final: 0.7807 (m-40)
REVERT: H   59 MET cc_start: 0.8924 (tpp) cc_final: 0.8396 (tpp)
REVERT: H   80 LEU cc_start: 0.9260 (tp) cc_final: 0.8989 (tp)
REVERT: K   63 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8762 (ttp-170)
REVERT: L   11 SER cc_start: 0.7528 (p) cc_final: 0.7237 (t)
  outliers start: 18
  outliers final: 16
  residues processed: 148
  average time/residue: 0.2897
  time to fit residues: 60.9095
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue   99 ILE
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  108 SER
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 116 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.156009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.121339 restraints weight = 33356.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.125354 restraints weight = 63344.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.125993 restraints weight = 23881.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3297
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3297
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14867  Z= 0.145
  Angle     :  0.548  12.946  21358  Z= 0.314
  Chirality :  0.034   0.158   2418
  Planarity :  0.004   0.048   1687
  Dihedral  : 29.437 174.792   4330
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.39 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.27), residues: 982
  helix:  2.74 (0.21), residues: 622
  sheet:  0.59 (0.96), residues: 30
  loop : -1.25 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L  93 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.012   0.001   PHE L  51 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.006   0.000   ARG C  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00033 (    2)
  link_TRANS           : angle       0.22511 (    6)
  hydrogen bonds       : bond        0.04177 (  816)
  hydrogen bonds       : angle       2.94771 ( 2081)
  metal coordination   : bond        0.00490 (    8)
  metal coordination   : angle       6.61353 (    9)
  covalent geometry    : bond        0.00317 (14857)
  covalent geometry    : angle       0.53095 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8797 (m-10) cc_final: 0.8527 (m-10)
REVERT: D   71 GLU cc_start: 0.8618 (tp30) cc_final: 0.8342 (tp30)
REVERT: F   25 ASN cc_start: 0.8044 (m110) cc_final: 0.7664 (m-40)
REVERT: L   11 SER cc_start: 0.7583 (p) cc_final: 0.7278 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 152
  average time/residue: 0.2673
  time to fit residues: 58.7360
Evaluate side-chains
  138 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  108 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0040
   chunk 8 optimal weight:    0.0970
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.158757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.120019 restraints weight = 21349.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.119397 restraints weight = 30397.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.119825 restraints weight = 28891.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14867  Z= 0.133
  Angle     :  0.542  14.199  21358  Z= 0.308
  Chirality :  0.033   0.138   2418
  Planarity :  0.004   0.040   1687
  Dihedral  : 29.286 176.401   4330
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.44 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.28), residues: 982
  helix:  2.92 (0.21), residues: 622
  sheet:  0.40 (0.97), residues: 30
  loop : -1.14 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L  93 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.010   0.001   PHE L  51 
 TYR   0.014   0.001   TYR K  64 
 ARG   0.004   0.000   ARG C  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00069 (    2)
  link_TRANS           : angle       0.18964 (    6)
  hydrogen bonds       : bond        0.03934 (  816)
  hydrogen bonds       : angle       2.83963 ( 2081)
  metal coordination   : bond        0.00587 (    8)
  metal coordination   : angle       5.95308 (    9)
  covalent geometry    : bond        0.00284 (14857)
  covalent geometry    : angle       0.52814 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8660 (m-10) cc_final: 0.8339 (m-10)
REVERT: D   59 MET cc_start: 0.8944 (tpp) cc_final: 0.8570 (tpp)
REVERT: D   71 GLU cc_start: 0.8561 (tp30) cc_final: 0.8335 (tp30)
REVERT: F   25 ASN cc_start: 0.7831 (m110) cc_final: 0.7508 (m-40)
REVERT: L   11 SER cc_start: 0.6979 (p) cc_final: 0.6591 (t)
  outliers start: 16
  outliers final: 12
  residues processed: 150
  average time/residue: 0.2669
  time to fit residues: 57.5485
Evaluate side-chains
  148 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 99 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0770
   chunk 28 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0030
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.3348

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN
L  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.157829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.124314 restraints weight = 29220.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.123645 restraints weight = 50940.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.124589 restraints weight = 45587.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14867  Z= 0.130
  Angle     :  0.536  14.055  21358  Z= 0.305
  Chirality :  0.032   0.133   2418
  Planarity :  0.004   0.038   1687
  Dihedral  : 29.233 177.234   4330
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.19 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.27), residues: 982
  helix:  2.97 (0.21), residues: 623
  sheet:  0.38 (0.98), residues: 30
  loop : -1.13 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  93 
 HIS   0.003   0.001   HIS K  65 
 PHE   0.011   0.001   PHE K  53 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.003   0.000   ARG D  79 

Details of bonding type rmsd
  link_TRANS           : bond        0.00063 (    2)
  link_TRANS           : angle       0.21894 (    6)
  hydrogen bonds       : bond        0.03837 (  816)
  hydrogen bonds       : angle       2.80331 ( 2081)
  metal coordination   : bond        0.00406 (    8)
  metal coordination   : angle       5.66221 (    9)
  covalent geometry    : bond        0.00274 (14857)
  covalent geometry    : angle       0.52311 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8710 (m-10) cc_final: 0.8440 (m-10)
REVERT: D   59 MET cc_start: 0.8866 (tpp) cc_final: 0.8482 (tpp)
REVERT: D   71 GLU cc_start: 0.8606 (tp30) cc_final: 0.8396 (tp30)
REVERT: D   79 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8204 (ttm-80)
REVERT: F   25 ASN cc_start: 0.7980 (m110) cc_final: 0.7600 (m-40)
REVERT: H   59 MET cc_start: 0.8640 (tpp) cc_final: 0.8229 (tpp)
REVERT: L   11 SER cc_start: 0.7046 (p) cc_final: 0.6654 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 145
  average time/residue: 0.2788
  time to fit residues: 57.7779
Evaluate side-chains
  141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 45 optimal weight:    0.0050
   chunk 35 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.6994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.158571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.121340 restraints weight = 23371.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.120727 restraints weight = 38098.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.121227 restraints weight = 33149.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3330
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14867  Z= 0.138
  Angle     :  0.548  14.172  21358  Z= 0.309
  Chirality :  0.033   0.131   2418
  Planarity :  0.004   0.036   1687
  Dihedral  : 29.285 177.444   4330
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.96 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.27), residues: 982
  helix:  2.97 (0.21), residues: 621
  sheet:  0.43 (1.00), residues: 30
  loop : -1.10 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  93 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.012   0.001   PHE L  51 
 TYR   0.022   0.001   TYR K  64 
 ARG   0.006   0.000   ARG C  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00026 (    2)
  link_TRANS           : angle       0.19668 (    6)
  hydrogen bonds       : bond        0.04118 (  816)
  hydrogen bonds       : angle       2.83608 ( 2081)
  metal coordination   : bond        0.00463 (    8)
  metal coordination   : angle       5.61904 (    9)
  covalent geometry    : bond        0.00302 (14857)
  covalent geometry    : angle       0.53552 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8642 (m-10) cc_final: 0.8393 (m-10)
REVERT: D   71 GLU cc_start: 0.8549 (tp30) cc_final: 0.8293 (tp30)
REVERT: F   25 ASN cc_start: 0.7841 (m110) cc_final: 0.7524 (m-40)
REVERT: H   59 MET cc_start: 0.8557 (tpp) cc_final: 0.8138 (tpp)
REVERT: K   64 TYR cc_start: 0.8037 (t80) cc_final: 0.7344 (t80)
REVERT: L   11 SER cc_start: 0.6875 (p) cc_final: 0.6464 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 140
  average time/residue: 0.2725
  time to fit residues: 54.9805
Evaluate side-chains
  143 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 114 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 110 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   overall best weight:    2.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.147362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.099216 restraints weight = 34184.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.100448 restraints weight = 23085.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.100561 restraints weight = 16688.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  14867  Z= 0.230
  Angle     :  0.637  13.574  21358  Z= 0.356
  Chirality :  0.037   0.138   2418
  Planarity :  0.004   0.033   1687
  Dihedral  : 29.802 174.308   4330
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.31 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.27), residues: 982
  helix:  2.56 (0.21), residues: 623
  sheet:  0.38 (1.01), residues: 30
  loop : -1.29 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L  93 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.010   0.002   PHE D  65 
 TYR   0.021   0.002   TYR H  83 
 ARG   0.009   0.001   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00130 (    2)
  link_TRANS           : angle       0.16941 (    6)
  hydrogen bonds       : bond        0.05838 (  816)
  hydrogen bonds       : angle       3.22517 ( 2081)
  metal coordination   : bond        0.00962 (    8)
  metal coordination   : angle       6.46143 (    9)
  covalent geometry    : bond        0.00541 (14857)
  covalent geometry    : angle       0.62329 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8829 (m-10) cc_final: 0.8622 (m-10)
REVERT: C   35 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7662 (mtt180)
REVERT: C   73 ASN cc_start: 0.8725 (t0) cc_final: 0.8418 (t0)
REVERT: F   25 ASN cc_start: 0.8401 (m110) cc_final: 0.7930 (m-40)
REVERT: K   63 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8491 (ttp-170)
  outliers start: 12
  outliers final: 11
  residues processed: 141
  average time/residue: 0.2933
  time to fit residues: 58.5402
Evaluate side-chains
  136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 64 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 110 optimal weight:    8.9990
   chunk 68 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 102 optimal weight:   30.0000
   chunk 118 optimal weight:    2.9990
   overall best weight:    0.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.151866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.103444 restraints weight = 29163.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.105531 restraints weight = 20542.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.105582 restraints weight = 13871.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14867  Z= 0.146
  Angle     :  0.573  14.982  21358  Z= 0.322
  Chirality :  0.034   0.220   2418
  Planarity :  0.004   0.037   1687
  Dihedral  : 29.456 175.558   4330
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.89 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.27), residues: 982
  helix:  2.82 (0.21), residues: 622
  sheet:  0.28 (1.02), residues: 30
  loop : -1.16 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP L  93 
 HIS   0.007   0.001   HIS D  82 
 PHE   0.014   0.001   PHE L  51 
 TYR   0.019   0.001   TYR B  88 
 ARG   0.004   0.000   ARG C  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00021 (    2)
  link_TRANS           : angle       0.19053 (    6)
  hydrogen bonds       : bond        0.04324 (  816)
  hydrogen bonds       : angle       2.98220 ( 2081)
  metal coordination   : bond        0.00469 (    8)
  metal coordination   : angle       6.14014 (    9)
  covalent geometry    : bond        0.00318 (14857)
  covalent geometry    : angle       0.55871 (21343)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7694 (pm20)
REVERT: B   98 TYR cc_start: 0.8873 (m-10) cc_final: 0.8593 (m-10)
REVERT: C   73 ASN cc_start: 0.8673 (t0) cc_final: 0.8378 (t0)
REVERT: D   71 GLU cc_start: 0.8789 (tp30) cc_final: 0.8527 (tp30)
REVERT: F   25 ASN cc_start: 0.8375 (m110) cc_final: 0.7864 (m-40)
REVERT: H   59 MET cc_start: 0.8612 (tpp) cc_final: 0.8361 (tpp)
REVERT: L   11 SER cc_start: 0.8064 (t) cc_final: 0.7781 (p)
  outliers start: 13
  outliers final: 11
  residues processed: 147
  average time/residue: 0.2909
  time to fit residues: 61.6251
Evaluate side-chains
  145 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   83 TYR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    2.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.146361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.097619 restraints weight = 31072.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.099462 restraints weight = 22049.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.099312 restraints weight = 15358.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  14867  Z= 0.245
  Angle     :  0.652  13.927  21358  Z= 0.363
  Chirality :  0.038   0.240   2418
  Planarity :  0.005   0.034   1687
  Dihedral  : 29.860 172.770   4330
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.66 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.27), residues: 982
  helix:  2.48 (0.21), residues: 622
  sheet:  0.18 (0.99), residues: 30
  loop : -1.39 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP L  93 
 HIS   0.005   0.001   HIS G  31 
 PHE   0.011   0.002   PHE D  65 
 TYR   0.024   0.002   TYR H  83 
 ARG   0.004   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00151 (    2)
  link_TRANS           : angle       0.18387 (    6)
  hydrogen bonds       : bond        0.05930 (  816)
  hydrogen bonds       : angle       3.31325 ( 2081)
  metal coordination   : bond        0.00857 (    8)
  metal coordination   : angle       7.03679 (    9)
  covalent geometry    : bond        0.00580 (14857)
  covalent geometry    : angle       0.63649 (21343)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4099.24 seconds
wall clock time: 71 minutes 37.49 seconds (4297.49 seconds total)