Starting phenix.real_space_refine
on Thu May 15 21:24:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn2_40610/05_2025/8sn2_40610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn2_40610/05_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_40610/05_2025/8sn2_40610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn2_40610/05_2025/8sn2_40610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn2_40610/05_2025/8sn2_40610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn2_40610/05_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-5687/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: 3.52
  Conformation dependent library (CDL) restraints added in 1.4 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: 6.65
  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: 5.05

  Time building geometry restraints manager: 4.15 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:             0.840
  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:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     41.760
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.060
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.380
-------------------------------------------------------------------------------
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  : 1.082 
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: 0.2838
  time to fit residues: 73.6672
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  : 1.115 
-------------------------------------------------------------------------------
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 = 31019.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.123013 restraints weight = 61114.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123152 restraints weight = 25965.443|
|-----------------------------------------------------------------------------|
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 = 0.27   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  : 1.056 
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: 0.8250 (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: 0.2663
  time to fit residues: 58.7289
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  : 0.982 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 120 optimal weight:    6.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.155123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.122302 restraints weight = 34514.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125663 restraints weight = 66955.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.126187 restraints weight = 22919.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1350

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= 0.162
  Angle     :  0.569  14.669  21358  Z= 0.324
  Chirality :  0.034   0.209   2418
  Planarity :  0.004   0.040   1687
  Dihedral  : 29.424 175.518   4330
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.11 %
    Favored  : 87.13 %
  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:  2.05 (0.27), residues: 982
  helix:  2.67 (0.21), residues: 622
  sheet:  0.63 (0.95), residues: 30
  loop : -1.27 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP L  93 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.010   0.001   PHE L  51 
 TYR   0.008   0.001   TYR H  83 
 ARG   0.003   0.000   ARG C  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00009 (    2)
  link_TRANS           : angle       0.33351 (    6)
  hydrogen bonds       : bond        0.04644 (  816)
  hydrogen bonds       : angle       3.09663 ( 2081)
  metal coordination   : bond        0.00567 (    8)
  metal coordination   : angle       6.84834 (    9)
  covalent geometry    : bond        0.00363 (14857)
  covalent geometry    : angle       0.55116 (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
  156 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8804 (m-10) cc_final: 0.8466 (m-10)
REVERT: C   36 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8521 (mttp)
REVERT: D   71 GLU cc_start: 0.8584 (tp30) cc_final: 0.8328 (tp30)
REVERT: E   59 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7713 (pm20)
REVERT: F   25 ASN cc_start: 0.8042 (m110) cc_final: 0.7654 (m-40)
  outliers start: 15
  outliers final: 13
  residues processed: 146
  average time/residue: 0.2729
  time to fit residues: 57.3541
Evaluate side-chains
  144 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
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 K residue   74 VAL
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  108 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:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 118 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 112 optimal weight:   20.0000
   chunk 39 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.153470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.123524 restraints weight = 38443.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.125472 restraints weight = 74297.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.126685 restraints weight = 23358.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3297
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3297
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1630

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= 0.182
  Angle     :  0.580  14.053  21358  Z= 0.331
  Chirality :  0.035   0.213   2418
  Planarity :  0.004   0.048   1687
  Dihedral  : 29.609 174.487   4330
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.45 %
    Favored  : 84.91 %
  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:  1.96 (0.27), residues: 982
  helix:  2.62 (0.21), residues: 617
  sheet:  0.51 (0.94), residues: 30
  loop : -1.28 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L  93 
 HIS   0.005   0.001   HIS K  83 
 PHE   0.012   0.002   PHE L  51 
 TYR   0.016   0.002   TYR K  84 
 ARG   0.003   0.000   ARG A 116 

Details of bonding type rmsd
  link_TRANS           : bond        0.00038 (    2)
  link_TRANS           : angle       0.27247 (    6)
  hydrogen bonds       : bond        0.05019 (  816)
  hydrogen bonds       : angle       3.13836 ( 2081)
  metal coordination   : bond        0.00642 (    8)
  metal coordination   : angle       6.98963 (    9)
  covalent geometry    : bond        0.00418 (14857)
  covalent geometry    : angle       0.56229 (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
  153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8801 (m-10) cc_final: 0.8455 (m-10)
REVERT: C   36 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8588 (mttp)
REVERT: D   71 GLU cc_start: 0.8550 (tp30) cc_final: 0.8283 (tp30)
REVERT: F   25 ASN cc_start: 0.8117 (m110) cc_final: 0.7730 (m-40)
REVERT: H   80 LEU cc_start: 0.9252 (tp) cc_final: 0.9002 (tp)
REVERT: K   63 ARG cc_start: 0.9095 (ttp80) cc_final: 0.8741 (ttp-170)
REVERT: L   11 SER cc_start: 0.7598 (p) cc_final: 0.7300 (t)
  outliers start: 14
  outliers final: 13
  residues processed: 145
  average time/residue: 0.2808
  time to fit residues: 57.7236
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  : 1.015 
-------------------------------------------------------------------------------
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 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   80 SER
Chi-restraints excluded: chain L residue   94 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:    9.9990
   chunk 67 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 89 optimal weight:    6.9990
   chunk 116 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3806 r_free = 0.3806 target = 0.157057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.122226 restraints weight = 33382.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.126535 restraints weight = 63532.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.127272 restraints weight = 23497.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1657

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= 0.141
  Angle     :  0.540  12.557  21358  Z= 0.311
  Chirality :  0.033   0.222   2418
  Planarity :  0.004   0.038   1687
  Dihedral  : 29.337 175.688   4330
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.27 %
    Favored  : 83.74 %
  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:  2.79 (0.21), residues: 623
  sheet:  0.61 (0.96), residues: 30
  loop : -1.18 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP L  93 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.011   0.001   PHE L  51 
 TYR   0.009   0.001   TYR K  84 
 ARG   0.003   0.000   ARG D  79 

Details of bonding type rmsd
  link_TRANS           : bond        0.00047 (    2)
  link_TRANS           : angle       0.21850 (    6)
  hydrogen bonds       : bond        0.04068 (  816)
  hydrogen bonds       : angle       2.90720 ( 2081)
  metal coordination   : bond        0.00477 (    8)
  metal coordination   : angle       6.35348 (    9)
  covalent geometry    : bond        0.00307 (14857)
  covalent geometry    : angle       0.52377 (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
  157 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8785 (m-10) cc_final: 0.8434 (m-10)
REVERT: D   71 GLU cc_start: 0.8557 (tp30) cc_final: 0.8291 (tp30)
REVERT: F   25 ASN cc_start: 0.8036 (m110) cc_final: 0.7654 (m-40)
REVERT: L   11 SER cc_start: 0.7444 (p) cc_final: 0.7118 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 149
  average time/residue: 0.2640
  time to fit residues: 56.4963
Evaluate side-chains
  143 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  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 C residue  110 ASN
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 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:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0000
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.157098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.116871 restraints weight = 20431.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.116375 restraints weight = 32098.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.116756 restraints weight = 28177.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1765

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= 0.142
  Angle     :  0.548  13.415  21358  Z= 0.311
  Chirality :  0.033   0.210   2418
  Planarity :  0.004   0.038   1687
  Dihedral  : 29.349 176.046   4330
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.44 %
    Favored  : 82.46 %
  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:  2.28 (0.27), residues: 982
  helix:  2.85 (0.21), residues: 623
  sheet:  0.57 (0.99), residues: 30
  loop : -1.16 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP L  93 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.011   0.001   PHE L  51 
 TYR   0.020   0.001   TYR K  64 
 ARG   0.002   0.000   ARG D  79 

Details of bonding type rmsd
  link_TRANS           : bond        0.00022 (    2)
  link_TRANS           : angle       0.19750 (    6)
  hydrogen bonds       : bond        0.04204 (  816)
  hydrogen bonds       : angle       2.88292 ( 2081)
  metal coordination   : bond        0.00603 (    8)
  metal coordination   : angle       6.05313 (    9)
  covalent geometry    : bond        0.00310 (14857)
  covalent geometry    : angle       0.53374 (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
  155 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8721 (m-10) cc_final: 0.8370 (m-10)
REVERT: D   71 GLU cc_start: 0.8601 (tp30) cc_final: 0.8334 (tp30)
REVERT: F   25 ASN cc_start: 0.8112 (m110) cc_final: 0.7707 (m-40)
REVERT: H   59 MET cc_start: 0.8608 (tpp) cc_final: 0.8095 (tpp)
REVERT: L   11 SER cc_start: 0.7498 (p) cc_final: 0.7194 (t)
  outliers start: 18
  outliers final: 17
  residues processed: 145
  average time/residue: 0.2757
  time to fit residues: 57.4027
Evaluate side-chains
  150 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
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 G residue   92 GLU
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   22 SER
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  120 VAL
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:    0.0000
   chunk 99 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0000
   chunk 28 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0870
   overall best weight:    0.5568

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.157994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.124344 restraints weight = 29110.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.123954 restraints weight = 49571.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.124974 restraints weight = 43554.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1805

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= 0.135
  Angle     :  0.544  13.585  21358  Z= 0.309
  Chirality :  0.033   0.203   2418
  Planarity :  0.004   0.038   1687
  Dihedral  : 29.285 176.696   4330
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.26 %
    Favored  : 81.64 %
  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:  2.39 (0.27), residues: 982
  helix:  2.93 (0.21), residues: 623
  sheet:  0.51 (0.99), residues: 30
  loop : -1.12 (0.31), residues: 329

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   0.012   0.001   PHE L  51 
 TYR   0.008   0.001   TYR H  40 
 ARG   0.003   0.000   ARG B  23 

Details of bonding type rmsd
  link_TRANS           : bond        0.00039 (    2)
  link_TRANS           : angle       0.19883 (    6)
  hydrogen bonds       : bond        0.04033 (  816)
  hydrogen bonds       : angle       2.84118 ( 2081)
  metal coordination   : bond        0.00455 (    8)
  metal coordination   : angle       5.93425 (    9)
  covalent geometry    : bond        0.00291 (14857)
  covalent geometry    : angle       0.53074 (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: 18
    poor density    : 132
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8722 (m-10) cc_final: 0.8399 (m-10)
REVERT: D   59 MET cc_start: 0.9000 (tpp) cc_final: 0.8708 (tpp)
REVERT: D   71 GLU cc_start: 0.8481 (tp30) cc_final: 0.8235 (tp30)
REVERT: F   25 ASN cc_start: 0.7927 (m110) cc_final: 0.7578 (m-40)
REVERT: H   59 MET cc_start: 0.8569 (tpp) cc_final: 0.8001 (tpp)
REVERT: L   11 SER cc_start: 0.7063 (p) cc_final: 0.6679 (t)
  outliers start: 18
  outliers final: 17
  residues processed: 141
  average time/residue: 0.2655
  time to fit residues: 54.0957
Evaluate side-chains
  147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
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 E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
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   89 LEU
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  120 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 45 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 60 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.155997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.117801 restraints weight = 22382.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.116967 restraints weight = 32739.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.117431 restraints weight = 31535.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1911

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= 0.154
  Angle     :  0.563  13.782  21358  Z= 0.319
  Chirality :  0.034   0.199   2418
  Planarity :  0.004   0.036   1687
  Dihedral  : 29.402 176.378   4330
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.02 %
    Favored  : 81.75 %
  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:  2.30 (0.27), residues: 982
  helix:  2.89 (0.21), residues: 622
  sheet:  0.40 (0.98), residues: 30
  loop : -1.17 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L  93 
 HIS   0.003   0.001   HIS K  65 
 PHE   0.012   0.001   PHE L  51 
 TYR   0.023   0.001   TYR K  64 
 ARG   0.003   0.000   ARG D  79 

Details of bonding type rmsd
  link_TRANS           : bond        0.00024 (    2)
  link_TRANS           : angle       0.17399 (    6)
  hydrogen bonds       : bond        0.04522 (  816)
  hydrogen bonds       : angle       2.92472 ( 2081)
  metal coordination   : bond        0.00615 (    8)
  metal coordination   : angle       6.01138 (    9)
  covalent geometry    : bond        0.00346 (14857)
  covalent geometry    : angle       0.55001 (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
  154 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7619 (pm20)
REVERT: B   98 TYR cc_start: 0.8742 (m-10) cc_final: 0.8464 (m-10)
REVERT: D   71 GLU cc_start: 0.8579 (tp30) cc_final: 0.8325 (tp30)
REVERT: F   25 ASN cc_start: 0.8102 (m110) cc_final: 0.7711 (m-40)
REVERT: L   11 SER cc_start: 0.7386 (p) cc_final: 0.7047 (t)
  outliers start: 19
  outliers final: 18
  residues processed: 144
  average time/residue: 0.2749
  time to fit residues: 56.4316
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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 C residue  110 ASN
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 E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
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   22 SER
Chi-restraints excluded: chain L residue   89 LEU
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  120 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 72 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.155527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.121210 restraints weight = 33927.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.125046 restraints weight = 67054.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125943 restraints weight = 24272.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1985

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= 0.158
  Angle     :  0.576  14.263  21358  Z= 0.324
  Chirality :  0.034   0.194   2418
  Planarity :  0.004   0.035   1687
  Dihedral  : 29.410 176.170   4330
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.73 %
    Favored  : 80.94 %
  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:  2.29 (0.27), residues: 982
  helix:  2.89 (0.21), residues: 617
  sheet:  0.35 (0.98), residues: 30
  loop : -1.13 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  93 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.013   0.001   PHE L  51 
 TYR   0.014   0.001   TYR H  83 
 ARG   0.005   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00025 (    2)
  link_TRANS           : angle       0.15400 (    6)
  hydrogen bonds       : bond        0.04511 (  816)
  hydrogen bonds       : angle       2.94580 ( 2081)
  metal coordination   : bond        0.00588 (    8)
  metal coordination   : angle       5.87893 (    9)
  covalent geometry    : bond        0.00357 (14857)
  covalent geometry    : angle       0.56383 (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
  153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8779 (m-10) cc_final: 0.8508 (m-10)
REVERT: D   71 GLU cc_start: 0.8523 (tp30) cc_final: 0.8294 (tp30)
REVERT: F   25 ASN cc_start: 0.8104 (m110) cc_final: 0.7708 (m-40)
REVERT: H   59 MET cc_start: 0.8742 (tpp) cc_final: 0.8230 (tpp)
REVERT: K   63 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8771 (ttp-170)
REVERT: L   11 SER cc_start: 0.7340 (p) cc_final: 0.7010 (t)
REVERT: L   90 ARG cc_start: 0.6585 (mtp-110) cc_final: 0.6379 (mtp180)
  outliers start: 20
  outliers final: 19
  residues processed: 143
  average time/residue: 0.2771
  time to fit residues: 56.0448
Evaluate side-chains
  148 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
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 C residue  110 ASN
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 E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
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   22 SER
Chi-restraints excluded: chain L residue   89 LEU
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  120 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 110 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.156603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.123305 restraints weight = 28617.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122493 restraints weight = 51434.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.123282 restraints weight = 47175.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2018

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= 0.146
  Angle     :  0.571  14.590  21358  Z= 0.320
  Chirality :  0.034   0.193   2418
  Planarity :  0.004   0.038   1687
  Dihedral  : 29.374 176.411   4330
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.61 %
    Favored  : 81.05 %
  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:  2.31 (0.27), residues: 982
  helix:  2.90 (0.21), residues: 617
  sheet:  0.31 (0.99), residues: 30
  loop : -1.12 (0.31), residues: 335

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   0.012   0.001   PHE L  51 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.007   0.000   ARG L  90 

Details of bonding type rmsd
  link_TRANS           : bond        0.00027 (    2)
  link_TRANS           : angle       0.17584 (    6)
  hydrogen bonds       : bond        0.04310 (  816)
  hydrogen bonds       : angle       2.92385 ( 2081)
  metal coordination   : bond        0.00502 (    8)
  metal coordination   : angle       5.83101 (    9)
  covalent geometry    : bond        0.00322 (14857)
  covalent geometry    : angle       0.55814 (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: 20
    poor density    : 131
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8751 (m-10) cc_final: 0.8465 (m-10)
REVERT: D   71 GLU cc_start: 0.8538 (tp30) cc_final: 0.8281 (tp30)
REVERT: F   25 ASN cc_start: 0.7976 (m110) cc_final: 0.7628 (m-40)
REVERT: H   59 MET cc_start: 0.8614 (tpp) cc_final: 0.8138 (tpp)
REVERT: L   11 SER cc_start: 0.7116 (p) cc_final: 0.6733 (t)
  outliers start: 20
  outliers final: 20
  residues processed: 140
  average time/residue: 0.2693
  time to fit residues: 54.2801
Evaluate side-chains
  148 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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 C residue  110 ASN
Chi-restraints excluded: chain C residue  118 LYS
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 E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
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   22 SER
Chi-restraints excluded: chain L residue   89 LEU
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  120 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0370
   chunk 83 optimal weight:    5.9990
   overall best weight:    2.1862

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.147281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.099006 restraints weight = 30924.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.100520 restraints weight = 22639.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.100484 restraints weight = 16074.939|
|-----------------------------------------------------------------------------|
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 = 0.16   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 = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  14867  Z= 0.229
  Angle     :  0.641  13.594  21358  Z= 0.358
  Chirality :  0.038   0.190   2418
  Planarity :  0.005   0.036   1687
  Dihedral  : 29.797 173.615   4330
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.73 %
    Favored  : 81.17 %
  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:  2.61 (0.21), residues: 617
  sheet:  0.22 (0.99), residues: 30
  loop : -1.32 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  93 
 HIS   0.006   0.001   HIS G  31 
 PHE   0.011   0.002   PHE D  65 
 TYR   0.023   0.002   TYR H  83 
 ARG   0.004   0.000   ARG A 116 

Details of bonding type rmsd
  link_TRANS           : bond        0.00113 (    2)
  link_TRANS           : angle       0.14152 (    6)
  hydrogen bonds       : bond        0.05759 (  816)
  hydrogen bonds       : angle       3.23289 ( 2081)
  metal coordination   : bond        0.00956 (    8)
  metal coordination   : angle       6.64024 (    9)
  covalent geometry    : bond        0.00541 (14857)
  covalent geometry    : angle       0.62681 (21343)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3809.15 seconds
wall clock time: 67 minutes 21.67 seconds (4041.67 seconds total)